Structural and thermodynamic analysis of modified nucleosides in self-assembled DNA cross-tiles.

PubMed

Hakker, Lauren; Marchi, Alexandria N; Harris, Kimberly A; LaBean, Thomas H; Agris, Paul F

2014-01-01

DNA Holliday junctions are important natural strand-exchange structures that form during homologous recombination. Immobile four-arm junctions, analogs to Holliday junctions, have been designed to self-assemble into cross-tile structures by maximizing Watson-Crick base pairing and fixed crossover points. The cross-tiles, self-assembled from base pair recognition between designed single-stranded DNAs, form higher order lattice structures through cohesion of self-associating sticky ends. These cross-tiles have 16 unpaired nucleosides in the central loop at the junction of the four duplex stems. The importance of the centralized unpaired nucleosides to the structure's thermodynamic stability and self-assembly is unknown. Cross-tile DNA nanostructures were designed and constructed from nine single-stranded DNAs with four shell strands, four arms, and a central loop containing 16 unpaired bases. The 16 unpaired bases were either 2'-deoxyribothymidines, 2'-O-methylribouridines, or abasic 1',2'-dideoxyribonucleosides. Thermodynamic profiles and structural base-stacking contributions were assessed using UV absorption spectroscopy during thermal denaturation and circular dichroism spectroscopy, respectively, and the resulting structures were observed by atomic force microscopy. There were surprisingly significant changes in the thermodynamic and structural properties of lattice formation as a result of altering only the 16 unpaired, centralized nucleosides. The 16 unpaired 2'-O-methyluridines were stabilizing and produced uniform tubular structures. In contrast, the abasic nucleosides were destabilizing producing a mixture of structures. These results strongly indicate the importance of a small number of centrally located unpaired nucleosides within the structures. Since minor modifications lead to palpable changes in lattice formation, DNA cross-tiles present an easily manipulated structure convenient for applications in biomedical and biosensing devices.

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

PubMed

Yang, Changwon; Kim, Eunae; Pak, Youngshang

2015-09-18

Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson-Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine-thymine (A-T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Understanding the impact of the central atom on the ionic liquid behavior: phosphonium vs ammonium cations.

PubMed

Carvalho, Pedro J; Ventura, Sónia P M; Batista, Marta L S; Schröder, Bernd; Gonçalves, Fernando; Esperança, José; Mutelet, Fabrice; Coutinho, João A P

2014-02-14

The influence of the cation's central atom in the behavior of pairs of ammonium- and phosphonium-based ionic liquids was investigated through the measurement of densities, viscosities, melting temperatures, activity coefficients at infinite dilution, refractive indices, and toxicity against Vibrio fischeri. All the properties investigated are affected by the cation's central atom nature, with ammonium-based ionic liquids presenting higher densities, viscosities, melting temperatures, and enthalpies. Activity coefficients at infinite dilution show the ammonium-based ionic liquids to present slightly higher infinite dilution activity coefficients for non-polar solvents, becoming slightly lower for polar solvents, suggesting that the ammonium-based ionic liquids present somewhat higher polarities. In good agreement these compounds present lower toxicities than the phosphonium congeners. To explain this behavior quantum chemical gas phase DFT calculations were performed on isolated ion pairs at the BP-TZVP level of theory. Electronic density results were used to derive electrostatic potentials of the identified minimum conformers. Electrostatic potential-derived CHelpG and Natural Population Analysis charges show the P atom of the tetraalkylphosphonium-based ionic liquids cation to be more positively charged than the N atom in the tetraalkylammonium-based analogous IL cation, and a noticeable charge delocalization occurring in the tetraalkylammonium cation, when compared with the respective phosphonium congener. It is argued that this charge delocalization is responsible for the enhanced polarity observed on the ammonium based ionic liquids explaining the changes in the thermophysical properties observed.

Understanding the impact of the central atom on the ionic liquid behavior: Phosphonium vs ammonium cations

NASA Astrophysics Data System (ADS)

Carvalho, Pedro J.; Ventura, Sónia P. M.; Batista, Marta L. S.; Schröder, Bernd; Gonçalves, Fernando; Esperança, José; Mutelet, Fabrice; Coutinho, João A. P.

2014-02-01

The influence of the cation's central atom in the behavior of pairs of ammonium- and phosphonium-based ionic liquids was investigated through the measurement of densities, viscosities, melting temperatures, activity coefficients at infinite dilution, refractive indices, and toxicity against Vibrio fischeri. All the properties investigated are affected by the cation's central atom nature, with ammonium-based ionic liquids presenting higher densities, viscosities, melting temperatures, and enthalpies. Activity coefficients at infinite dilution show the ammonium-based ionic liquids to present slightly higher infinite dilution activity coefficients for non-polar solvents, becoming slightly lower for polar solvents, suggesting that the ammonium-based ionic liquids present somewhat higher polarities. In good agreement these compounds present lower toxicities than the phosphonium congeners. To explain this behavior quantum chemical gas phase DFT calculations were performed on isolated ion pairs at the BP-TZVP level of theory. Electronic density results were used to derive electrostatic potentials of the identified minimum conformers. Electrostatic potential-derived CHelpG and Natural Population Analysis charges show the P atom of the tetraalkylphosphonium-based ionic liquids cation to be more positively charged than the N atom in the tetraalkylammonium-based analogous IL cation, and a noticeable charge delocalization occurring in the tetraalkylammonium cation, when compared with the respective phosphonium congener. It is argued that this charge delocalization is responsible for the enhanced polarity observed on the ammonium based ionic liquids explaining the changes in the thermophysical properties observed.

The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli

PubMed Central

Beisel, Chase L.; Storz, Gisela

2011-01-01

SUMMARY Bacteria selectively consume some carbon sources over others through a regulatory mechanism termed catabolite repression. Here, we show that the base pairing RNA Spot 42 plays a broad role in catabolite repression in Escherichia coli by directly repressing genes involved in central and secondary metabolism, redox balancing, and the consumption of diverse non-preferred carbon sources. Many of the genes repressed by Spot 42 are transcriptionally activated by the global regulator CRP. Since CRP represses Spot 42, these regulators participate in a specific regulatory circuit called a multi-output feedforward loop. We found that this loop can reduce leaky expression of target genes in the presence of glucose and can maintain repression of target genes under changing nutrient conditions. Our results suggest that base pairing RNAs in feedforward loops can help shape the steady-state levels and dynamics of gene expression. PMID:21292161

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

NASA Astrophysics Data System (ADS)

Tangri, V.; Harvey-Thompson, A. J.; Giuliani, J. L.; Thornhill, J. W.; Velikovich, A. L.; Apruzese, J. P.; Ouart, N. D.; Dasgupta, A.; Jones, B.; Jennings, C. A.

2016-10-01

Radiation-magnetohydrodynamic simulations using the non-local thermodynamic equilibrium Mach2-Tabular Collisional-Radiative Equilibrium code in (r, z) geometry are performed for two pairs of recent Ar gas-puff Z-pinch experiments on the refurbished Z generator with an 8 cm diameter nozzle. One pair of shots had an outer-to-inner shell mass ratio of 1:1.6 and a second pair had a ratio of 1:1. In each pair, one of the shots had a central jet. The experimental trends in the Ar K-shell yield and power are reproduced in the calculations. However, the K-shell yield and power are significantly lower than the other three shots for the case of a double-shell puff of 1:1 mass ratio and no central jet configuration. Further simulations of a hypothetical experiment with the same relative density profile of this configuration, but higher total mass, show that the coupled energy from the generator and the K-shell yield can be increased to levels achieved in the other three configurations, but not the K-shell power. Based on various measures of effective plasma radius, the compression in the 1:1 mass ratio and no central jet case is found to be less because the plasma inside the magnetic piston is hotter and of lower density. Because of the reduced density, and the reduced radiation cooling (which is proportional to the square of the density), the core plasma is hotter. Consequently, for the 1:1 outer-to-inner shell mass ratio, the load mass controls the yield and the center jet controls the power.

Structure of the circumsporozoite protein gene in 18 strains of Plasmodium falciparum.

PubMed

Weber, J L; Hockmeyer, W T

1985-06-01

Using the cloned circumsporozoite (CS) protein gene of a Brazilian strain of Plasmodium falciparum as probe, we have analyzed the structure of the CS protein gene from 17 other Asian, African, Central and South American parasite strains by nucleic acid hybridization. Each strain appears to have one CS protein gene which hybridizes readily to the Brazilian strain probe. The 5' and 3' thirds of the genes are invariant in size in all 18 strains whereas the central third containing the 12 base pair tandem repeats varies in size over a range of about 100 base pairs. Several differences were found in the locations of Sau3A sites in the genes. The Sau3A sites are significant because each of the minority Asn-Val-Asp-Pro repeats in the cloned gene has a Sau3A site. DNA melting of hybrids revealed a high degree of homology between the sequences of the cloned gene and genes from an Asian strain and an African strain. A 14 base oligodeoxynucleotide with a sequence from the central repeat region hybridized to all strains tested. We conclude that the CS protein gene is highly conserved among strains of P. falciparum and that malaria vaccine development with the CS protein is unlikely to be complicated by strain variation.

Stacked-unstacked equilibrium at the nick site of DNA.

PubMed

Protozanova, Ekaterina; Yakovchuk, Peter; Frank-Kamenetskii, Maxim D

2004-09-17

Stability of duplex DNA with respect to separation of complementary strands is crucial for DNA executing its major functions in the cell and it also plays a central role in major biotechnology applications of DNA: DNA sequencing, polymerase chain reaction, and DNA microarrays. Two types of interaction are well known to contribute to DNA stability: stacking between adjacent base-pairs and pairing between complementary bases. However, their contribution into the duplex stability is yet to be determined. Now we fill this fundamental gap in our knowledge of the DNA double helix. We have prepared a series of 32, 300 bp-long DNA fragments with solitary nicks in the same position differing only in base-pairs flanking the nick. Electrophoretic mobility of these fragments in the gel has been studied. Assuming the equilibrium between stacked and unstacked conformations at the nick site, all 32 stacking free energy parameters have been obtained. Only ten of them are essential and they govern the stacking interactions between adjacent base-pairs in intact DNA double helix. A full set of DNA stacking parameters has been determined for the first time. From these data and from a well-known dependence of DNA melting temperature on G.C content, the contribution of base-pairing into duplex stability has been estimated. The obtained energy parameters of the DNA double helix are of paramount importance for understanding sequence-dependent DNA flexibility and for numerous biotechnology applications.

Glucose transporter distribution in the vessels of the central nervous system of the axolotl Ambystoma mexicanum (Urodela: Ambystomatidae).

PubMed

Lazzari, Maurizio; Bettini, Simone; Ciani, Franco; Franceschini, Valeria

2008-10-01

The GLUT-1 isoform of the glucose transporter is commonly considered a reliable molecular marker of blood-brain barrier endothelia in the neural vasculature organized in a three-dimensional network of single vessels. The central nervous system of the axolotl Ambystoma mexicanum is characterized by a vascular architecture that contains both single and paired vessels. The presence and distribution of the GLUT-1 transporter are studied in this urodele using both immunoperoxidase histochemistry and immunogold technique. Light microscopy reveals immunopositivity in both parenchymal and meningeal vessels. The transverse-sectioned pairs of vessels do not show the same size. Furthermore, in the same pair, the two elements often differ in diameter. The main regions of the central nervous system show a different percentage of the paired structures. Only immunogold cytochemistry reveals different staining intensity in the two adjoined elements of a vascular pair. Colloidal gold particles show an asymmetric distribution in the endothelia of both single and paired vessels. These particles are more numerous on the abluminal surface than on the luminal one. The particle density is calculated in both vascular types. The different values could indicate functional differences between single and paired vessels and between the two adjoined elements of a pair, regarding glucose transport.

Simultaneous transmission of wired and wireless signals based on double sideband carrier suppression

NASA Astrophysics Data System (ADS)

Bitew, Mekuanint Agegnehu; Shiu, Run-Kai; Peng, Peng-Chun; Wang, Cheng-Hao; Chen, Yan-Ming

2017-11-01

In this paper, we proposed and experimentally demonstrated simultaneous transmission of wired and wireless signals based on double sideband optical carrier suppression. By properly adjusting the bias point of the dual-output mach-zehnder modulator (MZM), a central carrier in one output port and a pair of first-order sidebands in another output port are generated. The pair of first-order sidebands are fed into a second MZM to generate second-order order sidebands. A wired signal is embedded on the central carrier while a wireless signal is embedded on the second-order sidebands. Unlike other schemes, we did not use optical filter to separate the carrier from the optical sidebands. The measured bit error rate (BER) and eye-diagrams after a 25 km single-mode-fiber (SMF) transmission proved that the proposed scheme is successful for both wired and wireless signals transmission. Moreover, the power penalty at the BER of 10-9 is 0.3 and 0.7 dB for wired and wireless signals, respectively.

NNLO corrections to top pair production at hadron colliders: the quark-gluon reaction

NASA Astrophysics Data System (ADS)

Czakon, Michal; Mitov, Alexander

2013-01-01

We compute the next-to-next-to-leading order QCD correction to the total inclusive top pair production cross-section in the reaction qgto toverline{t}+X . We find moderate {O} (1%) correction to central values at both Tevatron and LHC. The scale variation of the cross-section remains unchanged at the Tevatron and is significantly reduced at the LHC. We find that recently introduced approximation based on the high-energy limit of the top pair cross-section significantly deviates from the exact result. The results derived in the present work are included in version 1.4 of the program Top++. Work towards computing the reaction ggto toverline{t}+X is ongoing.

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

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

Ong, Tzen; Coleman, Piers; Schmalian, Jörg

A central question in iron-based superconductivity is the mechanism by which the paired electrons minimize their strong mutual Coulomb repulsion. In most unconventional superconductors, Coulomb repulsion is minimized through the formation of higher angular momentum Cooper pairs, with Fermi surface nodes in the pair wavefunction. The apparent absence of such nodes in the iron-based superconductors has led to a belief they form an s-wave (s ±) singlet state, which changes sign between the electron and hole pockets. However, the multiorbital nature of these systems opens an alternative possibility. In this paper, we propose a new class of s ± statemore » containing a condensate of d-wave Cooper pairs, concealed by their entanglement with the iron orbitals. By combining the d-wave (L=2) motion of the pairs with the internal angular momenta I =2 of the iron orbitals to make a singlet (J =L+I =0), an s ± superconductor with a nontrivial topology is formed. This scenario allows us to understand the development of octet nodes in potassium-doped Ba 1$-$xK XFe 2As 2 as a reconfiguration of the orbital and internal angular momentum into a high spin (J =L+I =4) state; the reverse transition under pressure into a fully gapped state can then be interpreted as a return to the low-spin singlet. Finally, the formation of orbitally entangled pairs is predicted to give rise to a shift in the orbital content at the Fermi surface, which can be tested via laser-based angle-resolved photoemission spectroscopy.« less

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

DOE PAGES

Ong, Tzen; Coleman, Piers; Schmalian, Jörg

2016-05-02

A central question in iron-based superconductivity is the mechanism by which the paired electrons minimize their strong mutual Coulomb repulsion. In most unconventional superconductors, Coulomb repulsion is minimized through the formation of higher angular momentum Cooper pairs, with Fermi surface nodes in the pair wavefunction. The apparent absence of such nodes in the iron-based superconductors has led to a belief they form an s-wave (s ±) singlet state, which changes sign between the electron and hole pockets. However, the multiorbital nature of these systems opens an alternative possibility. In this paper, we propose a new class of s ± statemore » containing a condensate of d-wave Cooper pairs, concealed by their entanglement with the iron orbitals. By combining the d-wave (L=2) motion of the pairs with the internal angular momenta I =2 of the iron orbitals to make a singlet (J =L+I =0), an s ± superconductor with a nontrivial topology is formed. This scenario allows us to understand the development of octet nodes in potassium-doped Ba 1$-$xK XFe 2As 2 as a reconfiguration of the orbital and internal angular momentum into a high spin (J =L+I =4) state; the reverse transition under pressure into a fully gapped state can then be interpreted as a return to the low-spin singlet. Finally, the formation of orbitally entangled pairs is predicted to give rise to a shift in the orbital content at the Fermi surface, which can be tested via laser-based angle-resolved photoemission spectroscopy.« less

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

PubMed

Ong, Tzen; Coleman, Piers; Schmalian, Jörg

2016-05-17

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

A Bulky Rhodium Complex Bound to an Adenosine-Adenosine DNA Mismatch: General Architecture of the Metalloinsertion Binding Mode†

PubMed Central

Zeglis, Brian M.; Pierre, Valérie C.; Kaiser, Jens T.; Barton, Jacqueline K.

2009-01-01

Two crystal structures are determined for Δ-Rh(bpy)2(chrysi)3+ (chrysi = 5,6-chrysenequinone diimine) bound to the oligonucleotide duplex 5′-CGGAAATTACCG-3′ containing two adenosine-adenosine mismatches (italics) through metalloinsertion. Diffraction quality crystals with two different space groups (P3221 and P43212) were obtained under very similar crystallization conditions. In both structures, the bulky rhodium complex inserts into the two mismatched sites from the minor groove side, ejecting the mismatched bases into the major groove. The conformational changes are localized to the mismatched site; the metal complex replaces the mismatched base pair without an increase in base pair rise. The expansive metal complex is accommodated in the duplex by a slight opening in the phosphodiester backbone; all sugars retain a C2′-endo puckering, and flanking base pairs neither stretch nor shear. The structures differ, however, in that in one of the structures, an additional metal complex is bound by intercalation from the major groove at the central 5′-AT-3′ step. We conclude that this additional metal complex is intercalated into this central step because of crystal packing forces. The structures described here of Δ-Rh(bpy)2(chrysi)3+ bound to thermodynamically destabilized AA mismatches share critical features with binding by metalloinsertion in two other oligonucleotides containing different single base mismatches. These results underscore the generality of the metalloinsertion as a new mode of non-covalent binding by small molecules with a DNA duplex. PMID:19374348

Mother-daughter correlation of central obesity and other noncommunicable disease risk factors: Tehran Lipid and Glucose Study.

PubMed

Heidari, Zahra; Hosseinpanah, Farhad; Barzin, Maryam; Safarkhani, Maryam; Azizi, Fereidoun

2015-03-01

This study aimed to investigate the mother-daughter correlation for central obesity and other noncommunicable disease risk factors. The authors used metabolic and anthropometric data from the Tehran Lipid and Glucose Study, enrolling 1041 mother-daughter pairs for the current study. Three age strata were defined: 3 to 9 years for childhood (146 mother-daughter pairs), 10 to 17 years for adolescence (395 mother-daughter pairs), and 18 to 25 years for early adulthood (500 mother-daughter pairs). Familial associations for central obesity and other noncommunicable disease risk factors were assessed. The prevalence of central obesity was 44.7% in mothers and 11.2% in daughters (6.2% in the 3-9, 19.2% in the 10-17, and 6.4% in the 18-25 years groups). Mothers with central obesity were more likely than nonobese mothers to have daughters with central obesity (10.5% and 1.7%, respectively; P = .0001). Central obesity indices among daughters were positively correlated with those of their mothers in all 3 age strata. Correlations for other noncommunicable disease risk factors were analyzed before and after adjusting the risk factor levels for mothers' and daughters' waist circumferences (WCs) within each group to determine whether risk factor correlations were, in part, a result of the central obesity correlations. After the non-communicable disease risk factor levels of participants were adjusted for their WCs, the mother-daughter correlations remained significant. The consistent association of central obesity between mothers and daughters may indicate the key role that could be played by the mother in the primary prevention of central obesity, particularly in high-risk families. © 2012 APJPH.

Saddle clamp assembly

NASA Technical Reports Server (NTRS)

Belrose, Charles R. (Inventor)

1994-01-01

A saddle clamp assembly is presented. The assembly is comprised of a hollow cylindrical body centered about a longitudinal axis and being diametrically split into semicircular top and bottom sections. Each section has a pair of connection flanges, at opposite ends, that project radially outward. A pair of bolts are retained on the top section flanges and are threadable into nuts retained on the bottom section flanges. A base member is anchored to a central underside portion of the bottom clamp body section and has a pair of connection tabs positioned beneath the bottom clamp body section connection flanges on opposite sides of the clamp axis. A pair of bolts are retained on the base member connection tabs and are threadable into a pair of nuts retainable on a support structure. The connection tab and connection flanges on each side of the clamp body are axially offset in a manner permitting downward installation/removable tool access to the lower bolts past the connection flanges. An elongated retention tether is used to connect the top clamp body section to the balance of the clamp assembly. This prevents loss of the top clamp body section when it is removed from the bottom clamp body section.

Kinship and Social Behavior of Lowland Tapirs (Tapirus terrestris) in a Central Amazon Landscape

PubMed Central

Pinho, Gabriela M.; Gonçalves da Silva, Anders; Hrbek, Tomas; Venticinque, Eduardo M.; Farias, Izeni P.

2014-01-01

We tested the hypothesis that tapirs tolerate individuals from adjacent and overlapping home ranges if they are related. We obtained genetic data from fecal samples collected in the Balbina reservoir landscape, central Amazon. Samples were genotyped at 14 microsatellite loci, of which five produced high quality informative genotypes. Based on an analysis of 32 individuals, we inferred a single panmictic population with high levels of heterozygosity. Kinship analysis identified 10 pairs of full siblings or parent-offspring, 10 pairs of half siblings and 25 unrelated pairs. In 10 cases, the related individuals were situated on opposite margins of the reservoir, suggesting that tapirs are capable of crossing the main river, even after damming. The polygamous model was the most likely mating system for Tapirus terrestris. Moran's I index of allele sharing between pairs of individuals geographically close (<3 km) was similar to that observed between individual pairs at larger distances (>3 km). Confirming this result, the related individuals were not geographically closer than unrelated ones (W = 188.5; p = 0.339). Thus, we found no evidence of a preference for being close to relatives and observed a tendency for dispersal. The small importance of relatedness in determining spatial distribution of individuals is unusual in mammals, but not unheard of. Finally, non-invasive sampling allowed efficient access to the genetic data, despite the warm and humid climate of the Amazon, which accelerates DNA degradation. PMID:24671057

Starbursts triggered by central overpressure in interacting galaxies

NASA Technical Reports Server (NTRS)

Jog, Chanda J.; Das, Mousumi

1993-01-01

A triggering mechanism for the origin of enhanced, massive-star formation in the central regions of interacting spiral galaxy pairs is proposed. Our mechanism is based on the detailed evolution of a realistic interstellar medium in a galaxy following an encounter. As a disk giant molecular cloud (GMC) tumbles into the central region following a galaxy encounter, it undergoes a radiative shock compression via the pre-existing high pressure of the central intercloud medium. The shocked outer shell of a GMC becomes gravitationally unstable and begins to fragment thus resulting in a burst of star formation, when the growth time for the gravitational instabilities in the shell becomes smaller than the crossing time of the shock. The resulting values of typical infrared luminosity agree with observations.

Pedagogies of Transformation for High School Study Abroad Programming

ERIC Educational Resources Information Center

Monaghan, Christine E.; Hartmann, Gennifre

2014-01-01

This autoethnographic case study examines the ways in which high school students and teachers' behaviors, values, and attitudes were transformed during their participation on a semester-long study abroad program in Central America. The study found that an integrative pedagogical approach in which place-based content was paired with place-based…

STAR results on central exclusive production in proton-proton collisions

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

Przybycien, Mariusz

2015-04-10

We present a preliminary measurement of the Central Exclusive Production of the two oppositely charged pions produced in the process pp → ppπ{sup +} π{sup −}, obtained with the STAR detector at RHIC at √(s)=200 GeV. Silicon strip detectors placed in Roman Pots were used for tagging forward protons while pion pair tracks were reconstructed in the STAR Time Projection Chamber. Predictions of models based on Regge phenomenology are compared to the spectra of the kinematical variables corrected for detector acceptance and efficiency.

Reversed-phase ion-pair liquid chromatography method for purification of duplex DNA with single base pair resolution

PubMed Central

Wysoczynski, Christina L.; Roemer, Sarah C.; Dostal, Vishantie; Barkley, Robert M.; Churchill, Mair E. A.; Malarkey, Christopher S.

2013-01-01

Obtaining quantities of highly pure duplex DNA is a bottleneck in the biophysical analysis of protein–DNA complexes. In traditional DNA purification methods, the individual cognate DNA strands are purified separately before annealing to form DNA duplexes. This approach works well for palindromic sequences, in which top and bottom strands are identical and duplex formation is typically complete. However, in cases where the DNA is non-palindromic, excess of single-stranded DNA must be removed through additional purification steps to prevent it from interfering in further experiments. Here we describe and apply a novel reversed-phase ion-pair liquid chromatography purification method for double-stranded DNA ranging in lengths from 17 to 51 bp. Both palindromic and non-palindromic DNA can be readily purified. This method has the unique ability to separate blunt double-stranded DNA from pre-attenuated (n-1, n-2, etc) synthesis products, and from DNA duplexes with single base pair overhangs. Additionally, palindromic DNA sequences with only minor differences in the central spacer sequence of the DNA can be separated, and the purified DNA is suitable for co-crystallization of protein–DNA complexes. Thus, double-stranded ion-pair liquid chromatography is a useful approach for duplex DNA purification for many applications. PMID:24013567

Mapping proteins in the presence of paralogs using units of coevolution

PubMed Central

2013-01-01

Background We study the problem of mapping proteins between two protein families in the presence of paralogs. This problem occurs as a difficult subproblem in coevolution-based computational approaches for protein-protein interaction prediction. Results Similar to prior approaches, our method is based on the idea that coevolution implies equal rates of sequence evolution among the interacting proteins, and we provide a first attempt to quantify this notion in a formal statistical manner. We call the units that are central to this quantification scheme the units of coevolution. A unit consists of two mapped protein pairs and its score quantifies the coevolution of the pairs. This quantification allows us to provide a maximum likelihood formulation of the paralog mapping problem and to cast it into a binary quadratic programming formulation. Conclusion CUPID, our software tool based on a Lagrangian relaxation of this formulation, makes it, for the first time, possible to compute state-of-the-art quality pairings in a few minutes of runtime. In summary, we suggest a novel alternative to the earlier available approaches, which is statistically sound and computationally feasible. PMID:24564758

Effects of ligand electronegativity on recoupled pair bonds with application to sulfurane precursors.

PubMed

Lindquist, Beth A; Woon, David E; Dunning, Thom H

2014-07-31

Recoupled pair bonds (RPBs) are conditional bonds-they only form for selected central atoms and ligands. A complete theoretical description of RPBs requires an understanding of the properties of the central atom and ligands that enable such bonds to be formed. In this work, we show that ligand electronegativity is positively correlated with recoupled pair bond strength for a variety of ligands interacting with the 3p(2) pair of sulfur. We also describe substituent (X) effects on the SF(a(4)Σ(-)) state by investigating X2SF species. These effects generally mirror those observed for covalently bound analogues, but we found that recoupled pair bonding can lead to breakdowns in the expected relationships among bond length, strength, and force constant for some of these species. Finally, we compare the properties of two molecules of practical interest that are bound by recoupled pair bonds: the dimethyl sulfur fluoride and hydroxide radicals (DMS-F and DMS-OH).

Contacts between the factor TUF and RPG sequences.

PubMed

Vignais, M L; Huet, J; Buhler, J M; Sentenac, A

1990-08-25

The yeast TUF factor binds specifically to RPG-like sequences involved in multiple functions at enhancers, silencers, and telomeres. We have characterized the interaction of TUF with its optimal binding sequence, rpg-1 (1-ACACCCATACATTT-14), using a gel DNA-binding assay in combination with methylation protection and mutagenesis experiments. As many as 10 base pairs appear to be engaged in factor binding. Analysis of a collection of 30 different RPG mutants demonstrated the importance of 8 base pairs at position 2, 3, 4, 5, 6, 7, 10, and 12 and the critical role of the central GC pair at position 5. Methylation protection data on four different natural sites confirmed a close contact at positions 4, 5, 6, and 10 and suggested additional contacts at base pairs 8, 12, and 13. The derived consensus sequence was RCAAYCCRYNCAYY. A quantitative band shift analysis was used to determine the equilibrium dissociation constant for the complex of TUF and its optimal binding site rpg-1. The specific dissociation constant (K8) was found to be 1.3 x 10(-11) M. The comparison of the K8 value with the dissociation constant obtained for nonspecific DNA sites (Kn8 = 8.7 x 10(-6) M) shows the high binding selectivity of TUF for its specific RPG target.

The structure of the L3 loop from the hepatitis delta virus ribozyme: a syn cytidine.

PubMed Central

Lynch, S R; Tinoco, I

1998-01-01

The structure of the L3 central hairpin loop isolated from the antigenomic sequence of the hepatitis delta virus ribozyme with the P2 and P3 stems from the ribozyme stacked on top of the loop has been determined by NMR spectroscopy. The 26 nt stem-loop structure contains nine base pairs and a 7 nt loop (5'-UCCUCGC-3'). This hairpin loop is critical for efficient catalysis in the intact ribozyme. The structure was determined using homonuclear and heteronuclear NMR techniques on non-labeled and15N-labeled RNA oligonucleotides. The overall root mean square deviation for the structure was 1.15 A (+/- 0.28 A) for the loop and the closing C.G base pair and 0.90 A (+/- 0.18 A) for the loop and the closing C.G base pair but without the lone purine in the loop, which is not well defined in the structure. The structure indicates a U.C base pair between the nucleotides on the 5'- and 3'-ends of the loop. This base pair is formed with a single hydrogen bond involving the cytosine exocyclic amino proton and the carbonyl O4 of the uracil. The most unexpected finding in the loop is a syn cytidine. While not unprecedented, syn pyrimidines are highly unusual. This one can be confidently established by intranucleotide distances between the ribose and the base determined by NMR spectroscopy. A similar study of the structure of this loop showed a somewhat different three-dimensional structure. A discussion of differences in the two structures, as well as possible sites of interaction with the cleavage site, will be presented. PMID:9461457

Nonthermal electron-positron pairs and cold matter in the central engines of active galactic nuclei

NASA Technical Reports Server (NTRS)

Zdziarski, Andrzej A.

1992-01-01

The nonthermal e(+/-) pair model of the central engine of active galactic nuclei (AGNs) is discussed. The model assumes that nonthermal e(+/-) pairs are accelerated to highly relativistic energies in a compact region close to the central black hole and in the vicinity of some cold matter. The model has a small number of free parameters and explains a large body of AGN observations from EUV to soft gamma-rays. In particular, the model explains the existence of the UV bump, the soft X-rays excess, the canonical hard X-ray power law, the spectral hardening above about 10 keV, and some of the variability patterns in the soft and hard X-rays. In addition, the model explains the spectral steepening above about 50 keV seen in NGC 4151.

Central region component1, a novel synaptonemal complex component, is essential for meiotic recombination initiation in rice.

PubMed

Miao, Chunbo; Tang, Ding; Zhang, Honggen; Wang, Mo; Li, Yafei; Tang, Shuzhu; Yu, Hengxiu; Gu, Minghong; Cheng, Zhukuan

2013-08-01

In meiosis, homologous recombination entails programmed DNA double-strand break (DSB) formation and synaptonemal complex (SC) assembly coupled with the DSB repair. Although SCs display extensive structural conservation among species, their components identified are poorly conserved at the sequence level. Here, we identified a novel SC component, designated central region component1 (CRC1), in rice (Oryza sativa). CRC1 colocalizes with ZEP1, the rice SC transverse filament protein, to the central region of SCs in a mutually dependent fashion. Consistent with this colocalization, CRC1 interacts with ZEP1 in yeast two-hybrid assays. CRC1 is orthologous to Saccharomyces cerevisiae pachytene checkpoint2 (Pch2) and Mus musculus THYROID receptor-interacting protein13 (TRIP13) and may be a conserved SC component. Additionally, we provide evidence that CRC1 is essential for meiotic DSB formation. CRC1 interacts with homologous pairing aberration in rice meiosis1 (PAIR1) in vitro, suggesting that these proteins act as a complex to promote DSB formation. PAIR2, the rice ortholog of budding yeast homolog pairing1, is required for homologous chromosome pairing. We found that CRC1 is also essential for the recruitment of PAIR2 onto meiotic chromosomes. The roles of CRC1 identified here have not been reported for Pch2 or TRIP13.

CENTRAL REGION COMPONENT1, a Novel Synaptonemal Complex Component, Is Essential for Meiotic Recombination Initiation in Rice[C][W

PubMed Central

Miao, Chunbo; Tang, Ding; Zhang, Honggen; Wang, Mo; Li, Yafei; Tang, Shuzhu; Yu, Hengxiu; Gu, Minghong; Cheng, Zhukuan

2013-01-01

In meiosis, homologous recombination entails programmed DNA double-strand break (DSB) formation and synaptonemal complex (SC) assembly coupled with the DSB repair. Although SCs display extensive structural conservation among species, their components identified are poorly conserved at the sequence level. Here, we identified a novel SC component, designated CENTRAL REGION COMPONENT1 (CRC1), in rice (Oryza sativa). CRC1 colocalizes with ZEP1, the rice SC transverse filament protein, to the central region of SCs in a mutually dependent fashion. Consistent with this colocalization, CRC1 interacts with ZEP1 in yeast two-hybrid assays. CRC1 is orthologous to Saccharomyces cerevisiae pachytene checkpoint2 (Pch2) and Mus musculus THYROID RECEPTOR-INTERACTING PROTEIN13 (TRIP13) and may be a conserved SC component. Additionally, we provide evidence that CRC1 is essential for meiotic DSB formation. CRC1 interacts with HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS1 (PAIR1) in vitro, suggesting that these proteins act as a complex to promote DSB formation. PAIR2, the rice ortholog of budding yeast homolog pairing1, is required for homologous chromosome pairing. We found that CRC1 is also essential for the recruitment of PAIR2 onto meiotic chromosomes. The roles of CRC1 identified here have not been reported for Pch2 or TRIP13. PMID:23943860

Breeding phenology and reproductive success of the Brandt's Cormorant at three nearshore colonies in central California, 1997-2001

USGS Publications Warehouse

Jones, Nathan M.; McChesney, Gerard; Parker, Michael W.; Yee, Julie L.; Carter, Harry R.; Golightly, Richard T.

2008-01-01

Brandt's Cormorant (Phalacrocorax penicillatus) breeding effort, phenology and success were studied in 1997-2001 at three colonies spanning approximately 200 km of the central California coast: Point Reyes (PR); Devil's Slide Rock and Mainland (DS); and Castle-Hurricane Colony Complex (CH). Breeding effort was reduced at all three colonies in the 1998 El Niño event. Mean clutch initiation dates differed significantly among colonies, with cormorants at the southernmost colony (CH) laying earliest, and those at the northernmost colony (PR) laying latest. Productivity at individual colonies varied greatly among years (range 0.7-2.5 fledglings per pair). Overall colony means were lowest (1.6 fledglings/pair) during the 1998 El Niño event and highest (2.5 fledglings/pair) in the 1999 La Niña event. Productivity at CH (1.7 fledglings/pair) was significantly lower than at PR (2.2 fledglings/pair), and interannual variation was greatest at CH. Late-nesting birds laid fewer eggs, hatched fewer chicks, and fledged fewer chicks per pair than early-nesters. The rapid rate of growth at some nearshore colonies in central California suggests immigration from elsewhere, most likely the large offshore colony at the South Farallon Islands. Variation in timing of breeding and reproductive success among colonies demonstrates a value in maintaining multiple study locations when assessing Brandt's Cormorant population parameters in the California Current System.

Coal planer. [13 claims

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

Bahre, K.; Nowak, H.D.

1977-05-24

A coal planer for use in an underground mine gallery comprises a central unit, a pair of loading heads arranged spaced from and to opposite sides of the central unit and a pair of intermediate units, respectively, located between the central unit and the loading heads and linked to the latter and the central unit. Each of the intermediate units is provided with a plurality of planning knives arranged vertically spaced from each other for cutting coal from the mine face during reciprocation of the coal planer in a direction parallel to the mine face, and with a bottom knifemore » adapted to cut into the sole of the mine gallery. 13 claims, 5 figures.« less

Distortions induced in double-stranded oligonucleotides by the binding of cis- or trans-diammine-dichloroplatinum(II) to the d(GTG) sequence.

PubMed Central

Anin, M F; Leng, M

1990-01-01

Conformational changes induced in double-stranded oligonucleotides by the binding of trans- or cis-diamminedichloro platinum(II) to the d(GTG) sequence have been characterized by means of melting temperatures, electrophoretic migrations in non-denaturing polyacrylamide gels, reactivities with the artificial nuclease Phenanthroline-copper and with chemical probes. The cis-platinum adduct behaves more as a centre of directed bend than as a hinge joint, the induced bend angle being of the order of 25-30 degrees. The double helix is locally denatured over 2 base pairs (corresponding to the platinated 5'G residue and the central T residue) and is distorted over 4-5 base pairs. The trans-platinum adduct behaves also more as a centre of directed bend than as a hinge joint, the induced bend angle being of the order of 60 degrees. The double helix is locally denatured over 4 base pairs (corresponding to the immediately 5'T residue adjacent to the adduct and to the three base residues of the adduct). Both the cis- and trans-platinum adducts decrease the thermal stability of the double helix. Images PMID:2388824

Interaction of influenza virus polymerase with viral RNA in the 'corkscrew' conformation.

PubMed

Flick, R; Hobom, G

1999-10-01

The influenza virus RNA (vRNA) promoter structure is known to consist of the 5'- and 3'-terminal sequences of the RNA, within very narrow boundaries of 16 and 15 nucleotides, respectively. A complete set of single nucleotide substitutions led to the previously proposed model of a binary hooked or 'corkscrew' conformation for the vRNA promoter when it interacts with the viral polymerase. This functional structure is confirmed here with a complete set of complementary double substitutions, of both the regular A:U and G:C type and also the G:U type of base-pair exchanges. The proposed structure consists of a six base-pair RNA rod in the distal element in conjunction with two stem-loop structures of two short-range base-pairs (positions 2-9; 3-8). These support an exposed tetranucleotide loop within each branch of the proximal element, in an overall oblique organization due to a central unpaired A residue at position 10 in the 5' sequence. Long-range base-pairing between the entire 5' and 3' branches, as required for an unmodified 'panhandle' model, has been excluded for the proximal element, while it is known to represent the mode of interaction within the distal element. A large number of short-range base-pair exchanges in the proximal element constitute promoter-up mutations, which show activities several times above that of the wild-type in reporter gene assays. The unique overall conformation and rather few invariant nucleotides appear to be the core elements in vRNA recognition by polymerase and also in viral ribonucleoprotein packaging, to allow discrimination against the background of other RNA molecules in the cell.

Modelling exclusive meson pair production at hadron colliders

NASA Astrophysics Data System (ADS)

Harland-Lang, L. A.; Khoze, V. A.; Ryskin, M. G.

2014-04-01

We present a study of the central exclusive production of light meson pairs, concentrating on the region of lower invariant masses of the central system and/or meson transverse momentum, where perturbative QCD cannot be reliably applied. We describe in detail a phenomenological model, using the tools of Regge theory, that may be applied with some success in this regime, and we present the new, publicly available, Dime Monte Carlo (MC) implementation of this for , and production. The MC implementation includes a fully differential treatment of the survival factor, which in general depends on all kinematic variables, as well as allows for the so far reasonably unconstrained model parameters to be set by the user. We present predictions for the Tevatron and LHC, discuss and estimate the size of the proton-dissociative background, and show how future measurements may further test this Regge-based approach, as well as the soft hadronic model required to calculate the survival factor, in particular in the presence of tagged protons.

[Clinical study on aconite prescriptions with incompatible herbs in different areas based on association rules and analysis on compatibility features].

PubMed

Zuo, Ting; Fan, Xin-sheng; Tian, Shuo; Jiang, Chen-xue; Chen, Fei

2015-03-01

To explore the current application and features of Aconite prescriptions with incompatible herbs in grade A class three hospitals in east China and central China through a clinical study and comparative analysis. Clinical prescriptions containing Aconite with incompatible herbs were collected. Association rules were utilized to analyze the compatible features of these herbs. This analysis found that the frequently used incompatible herba; pairs are Aconiti Lateralis Radix Praeparata-Pinelliae Rhizoma, with the support rate of 44.45%, occupying nearly half of the surveyed prescriptions; Pinelliae Rhizoma is the most frequently used herb in the two areas, with support rate up to 76.24%. Among the top 10 herbal pairs in the support rate, except for Aconiti Lateralis Radix Praeparata and Pinelliae Rhizoma, the top 10 herbs in Central China were mostly for warming the middle jiao and tonifying qi, such as Zingiberis Rhizoma, Atractylodis Macrocephalae Rhizoma and Codonopsis Radix; Whereas those in east China were mostly for activating and nourishing blood, such as Angelicae Sinensis Radix, Chuanxiong Rhizoma, and Salviae Miltiorrhizae Radix et Rhizoma. Among the top 10 herbal pairs in the support rate, except for Aconiti Lateralis Radix Praeparata-Pinelliae Rhizoma, the core herbal pairs applied in central China were mainly for resolving phlegm and warming the middle jiao, such as Pinelliae Rhizoma-Glycyrrhizae Radix et Rhizoma, Pinelliae Rhizoma-Zingiberis Rhizoma; Whereas those in east China were principally for activating blood and tonifying qi, like Atractylodis Macrocephalae Rhizoma and Pinelliae Rhizoma, Angelicae Sinensis Radix and Pinelliae Rhizoma. Among the core herbal groups in the two areas, the most frequently used herbal groups in the two areas are Aconiti Lateralis Radix Praeparata, Glycyrrhizae Radix et Rhizoma and Pinelliae Rhizoma with the support rate of 59.73%, accounting for the highest proportion among all of herbal groups. There are the combined clinical application of Aconite with incompatible herbs, mostly with Aconiti Lateralis Radix Praeparata-Pinelliae Rhizoma, but with differences in the combined application in east China and central China.

Network modeling of PM10 concentration in Malaysia

NASA Astrophysics Data System (ADS)

Supian, Muhammad Nazirul Aiman Abu; Bakar, Sakhinah Abu; Razak, Fatimah Abdul

2017-08-01

Air pollution is not a new phenomenon in Malaysia. The Department of Environment (DOE) monitors the country's ambient air quality through a network of 51 stations. The air quality is measured using the Air Pollution Index (API) which is mainly recorded based on the concentration of particulate matter, PM10 readings. The Continuous Air Quality Monitoring (CAQM) stations are located in various places across the country. In this study, a network model of air quality based on PM10 concen tration for selected CAQM stations in Malaysia has been developed. The model is built using a graph formulation, G = (V, E) where vertex, V is a set of CAQM stations and edges, E is a set of correlation values for each pair of vertices. The network measurements such as degree distributions, closeness centrality, and betweenness centrality are computed to analyse the behaviour of the network. As a result, a rank of CAQM stations has been produced based on their centrality characteristics.

Headset Bluetooth and cell phone based continuous central body temperature measurement system.

PubMed

Sanches, J Miguel; Pereira, Bruno; Paiva, Teresa

2010-01-01

The accurate measure of the central temperature is a very important physiologic indicator in several clinical applications, namely, in the characterization and diagnosis of sleep disorders. In this paper a simple system is described to continuously measure the body temperature at the ear. An electronic temperature sensor is coupled to the microphone of a common commercial auricular Bluetooth device that sends the temperature measurements to a mobile phone to which is paired. The measurements are stored at the mobile phone and periodically sent to a medical facility by email or SMS (short messaging service).

Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA pairs in RNA

PubMed Central

2015-01-01

Molecular mechanics with all-atom models was used to understand the conformational preference of tandem guanine-adenine (GA) noncanonical pairs in RNA. These tandem GA pairs play important roles in determining stability, flexibility, and structural dynamics of RNA tertiary structures. Previous solution structures showed that these tandem GA pairs adopt either imino (cis Watson–Crick/Watson–Crick A-G) or sheared (trans Hoogsteen/sugar edge A-G) conformations depending on the sequence and orientation of the adjacent closing base pairs. The solution structures (GCGGACGC)2 [Biochemistry, 1996, 35, 9677–9689] and (GCGGAUGC)2 [Biochemistry, 2007, 46, 1511–1522] demonstrate imino and sheared conformations for the two central GA pairs, respectively. These systems were studied using molecular dynamics and free energy change calculations for conformational changes, using umbrella sampling. For the structures to maintain their native conformations during molecular dynamics simulations, a modification to the standard Amber ff10 force field was required, which allowed the amino group of guanine to leave the plane of the base [J. Chem. Theory Comput., 2009, 5, 2088–2100] and form out-of-plane hydrogen bonds with a cross-strand cytosine or uracil. The requirement for this modification suggests the importance of out-of-plane hydrogen bonds in stabilizing the native structures. Free energy change calculations for each sequence demonstrated the correct conformational preference when the force field modification was used, but the extent of the preference is underestimated. PMID:24803859

Sequence-dependent DNA deformability studied using molecular dynamics simulations.

PubMed

Fujii, Satoshi; Kono, Hidetoshi; Takenaka, Shigeori; Go, Nobuhiro; Sarai, Akinori

2007-01-01

Proteins recognize specific DNA sequences not only through direct contact between amino acids and bases, but also indirectly based on the sequence-dependent conformation and deformability of the DNA (indirect readout). We used molecular dynamics simulations to analyze the sequence-dependent DNA conformations of all 136 possible tetrameric sequences sandwiched between CGCG sequences. The deformability of dimeric steps obtained by the simulations is consistent with that by the crystal structures. The simulation results further showed that the conformation and deformability of the tetramers can highly depend on the flanking base pairs. The conformations of xATx tetramers show the most rigidity and are not affected by the flanking base pairs and the xYRx show by contrast the greatest flexibility and change their conformations depending on the base pairs at both ends, suggesting tetramers with the same central dimer can show different deformabilities. These results suggest that analysis of dimeric steps alone may overlook some conformational features of DNA and provide insight into the mechanism of indirect readout during protein-DNA recognition. Moreover, the sequence dependence of DNA conformation and deformability may be used to estimate the contribution of indirect readout to the specificity of protein-DNA recognition as well as nucleosome positioning and large-scale behavior of nucleic acids.

Genetic diversity of the human head lice, Pediculus humanus capitis, among primary school girls in Saudi Arabia, with reference to their prevalence.

PubMed

Al-Shahrani, Sarah A; Alajmi, Reem A; Ayaad, Tahany H; Al-Shahrani, Mohammed A; Shaurub, El-Sayed H

2017-10-01

The present work aimed at investigating the genetic diversity of the head louse Pediculus humanus capitis (P. humanus capitis) among infested primary school girls at Bisha governorate, Saudi Arabia, based on the sequence of mitochondrial cytochrome b (mt cyt b) gene of 121 P. humanus capitis adults. Additionally, the prevalence of pediculosis capitis was surveyed. The results of sequencing were compared with the sequence of human head lice that are genotyped previously. Phylogenetic tree analysis showed the presence of 100% identity (n = 26) of louse specimens with clade A (prevalent worldwide) of the GenBank data base. Louse individuals (n = 50) showed 99.8% similarity with the same clade A reference having a single base pair difference. Also, a number of 22 louse individuals revealed 99.8% identity with clade B reference (prevalent in North and Central Americas, Europe, and Australia) with individual diversity in two base pairs. Moreover, 14 louse individual sequences revealed 99.4% identity with three base pair differences. It was concluded that moderate pediculosis (~13%) prevailed among the female students of the primary schools. It was age-and hair texture (straight or curly)-dependent. P. humanus capitis prevalence diversity is of clades A and B genotyping.

Myotonic Dystrophy Type 1 RNA Crystal Structures Reveal Heterogeneous 1×1 Nucleotide UU Internal Loop Conformations⊥

PubMed Central

Kumar, Amit; Park, HaJeung; Fang, Pengfei; Parkesh, Raman; Guo, Min; Nettles, Kendall W.; Disney, Matthew D.

2011-01-01

RNA internal loops often display a variety of conformations in solution. Herein, we visualize conformational heterogeneity in the context of the 5′CUG/3′GUC repeat motif present in the RNA that causes myotonic dystrophy type 1 (DM1). Specifically, two crystal structures are disclosed of a model DM1 triplet repeating construct, 5′r(UUGGGC(CUG)3GUCC)2, refined to 2.20 Å and 1.52 Å resolution. Here, differences in orientation of the 5′ dangling UU end between the two structures induce changes in the backbone groove width, which reveals that non-canonical 1×1 nucleotide UU internal loops can display an ensemble of pairing conformations. In the 2.20 Å structure, CUGa, the 5′UU forms one hydrogen-bonded pairs with a 5′UU of a neighboring helix in the unit cell to form a pseudo-infinite helix. The central 1×1 nucleotide UU internal loop has no hydrogen bonds, while the terminal 1×1 nucleotide UU internal loops each form a one hydrogen-bonded pair. In the 1.52 Å structure, CUGb, the 5′ UU dangling end is tucked into the major groove of the duplex. While the canonical paired bases show no change in base pairing, in CUGb the terminal 1×1 nucleotide UU internal loops form now two hydrogen-bonded pairs. Thus, the shift in major groove induced by the 5′UU dangling end alters non-canonical base patterns. Collectively, these structures indicate that 1×1 nucleotide UU internal loops in DM1 may sample multiple conformations in vivo. This observation has implications for the recognition of this RNA, and other repeating transcripts, by protein and small molecule ligands. PMID:21988728

Myotonic dystrophy type 1 RNA crystal structures reveal heterogeneous 1 × 1 nucleotide UU internal loop conformations.

PubMed

Kumar, Amit; Park, HaJeung; Fang, Pengfei; Parkesh, Raman; Guo, Min; Nettles, Kendall W; Disney, Matthew D

2011-11-15

RNA internal loops often display a variety of conformations in solution. Herein, we visualize conformational heterogeneity in the context of the 5'CUG/3'GUC repeat motif present in the RNA that causes myotonic dystrophy type 1 (DM1). Specifically, two crystal structures of a model DM1 triplet repeating construct, 5'r[UUGGGC(CUG)(3)GUCC](2), refined to 2.20 and 1.52 Å resolution are disclosed. Here, differences in the orientation of the 5' dangling UU end between the two structures induce changes in the backbone groove width, which reveals that noncanonical 1 × 1 nucleotide UU internal loops can display an ensemble of pairing conformations. In the 2.20 Å structure, CUGa, the 5' UU forms a one hydrogen-bonded pair with a 5' UU of a neighboring helix in the unit cell to form a pseudoinfinite helix. The central 1 × 1 nucleotide UU internal loop has no hydrogen bonds, while the terminal 1 × 1 nucleotide UU internal loops each form a one-hydrogen bond pair. In the 1.52 Å structure, CUGb, the 5' UU dangling end is tucked into the major groove of the duplex. While the canonically paired bases show no change in base pairing, in CUGb the terminal 1 × 1 nucleotide UU internal loops now form two hydrogen-bonded pairs. Thus, the shift in the major groove induced by the 5' UU dangling end alters noncanonical base patterns. Collectively, these structures indicate that 1 × 1 nucleotide UU internal loops in DM1 may sample multiple conformations in vivo. This observation has implications for the recognition of this RNA, and other repeating transcripts, by protein and small molecule ligands.

Myotonic Dystrophy Type 1 RNA Crystal Structures Reveal Heterogeneous 1 × 1 Nucleotide UU Internal Loop Conformations

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

Kumar, Amit; Park, HaJeung; Fang, Pengfei

2012-03-27

RNA internal loops often display a variety of conformations in solution. Herein, we visualize conformational heterogeneity in the context of the 5'CUG/3'GUC repeat motif present in the RNA that causes myotonic dystrophy type 1 (DM1). Specifically, two crystal structures of a model DM1 triplet repeating construct, 5'r[{und UU}GGGC(C{und U}G){sub 3}GUCC]{sub 2}, refined to 2.20 and 1.52 {angstrom} resolution are disclosed. Here, differences in the orientation of the 5' dangling UU end between the two structures induce changes in the backbone groove width, which reveals that noncanonical 1 x 1 nucleotide UU internal loops can display an ensemble of pairing conformations.more » In the 2.20 {angstrom} structure, CUGa, the 5' UU forms a one hydrogen-bonded pair with a 5' UU of a neighboring helix in the unit cell to form a pseudoinfinite helix. The central 1 x 1 nucleotide UU internal loop has no hydrogen bonds, while the terminal 1 x 1 nucleotide UU internal loops each form a one-hydrogen bond pair. In the 1.52 {angstrom} structure, CUGb, the 5' UU dangling end is tucked into the major groove of the duplex. While the canonically paired bases show no change in base pairing, in CUGb the terminal 1 x 1 nucleotide UU internal loops now form two hydrogen-bonded pairs. Thus, the shift in the major groove induced by the 5' UU dangling end alters noncanonical base patterns. Collectively, these structures indicate that 1 x 1 nucleotide UU internal loops in DM1 may sample multiple conformations in vivo. This observation has implications for the recognition of this RNA, and other repeating transcripts, by protein and small molecule ligands.« less

Identification of a Novel Deletion in AVP-NPII Gene in a Patient with Central Diabetes Insipidus.

PubMed

Deniz, Ferhat; Acar, Ceren; Saglar, Emel; Erdem, Beril; Karaduman, Tugce; Yonem, Arif; Cagiltay, Eylem; Ay, Seyit Ahmet; Mergen, Hatice

2015-01-01

Central Diabetes Insipidus (CDI) is caused by a deficiency of antidiuretic hormone and characterized by polyuria, polydipsia and inability to concentrate urine. Our objective was to present the results of the molecular analyses of AVP-neurophysin II (AVP-NPII) gene in a large familial neurohypophyseal (central) DI pedigree. A male patient and his family members were analyzed and the prospective clinical data were collected. The proband applied to hospital for eligibility to be a recruit in Armed Forces. The patient had severe polyuria (20 L/day), polydipsia (20.5 L/day), fatique, and deep thirstiness. CDI was confirmed with the water deprivation-desmopressin test according to an increase in urine osmolality from 162 mOsm/kg to 432 mOsm/kg after desmopressin acetate injection. To evaluate the coding regions of AVP-NPII gene, polymerase chain reactions were performed and amplified regions were submitted to direct sequence analysis. We detected a heterozygous three base pair deletion at codon 69-70 (207_209delGGC) in exon 2, which lead to a deletion of the amino acid alanine. A three-dimensional protein structure prediction was shown for the deleted AVP-NPII and compared with the wild type. The three base pair deletion may yield an abnormal AVP precursor in neurophysin moiety, but further functional analyses are needed to understand the function of the deleted protein. © 2015 by the Association of Clinical Scientists, Inc.

The loss of a hydrogen bond: Thermodynamic contributions of a non-standard nucleotide

PubMed Central

Jolley, Elizabeth A.

2017-01-01

Abstract Non-standard nucleotides are ubiquitous in RNA. Thermodynamic studies with RNA duplexes containing non-standard nucleotides, whether incorporated naturally or chemically, can provide insight into the stability of Watson–Crick pairs and the role of specific functional groups in stabilizing a Watson–Crick pair. For example, an A-U, inosine•U and pseudouridine•A pair each form two hydrogen bonds. However, an RNA duplex containing a central I•U pair or central Ψ•A pair is 2.4 kcal/mol less stable or 1.7 kcal/mol more stable, respectively, than the corresponding duplex containing an A-U pair. In the non-standard nucleotide purine, hydrogen replaces the exocyclic amino group of A. This replacement results in a P•U pair containing only one hydrogen bond. Optical melting studies were performed with RNA duplexes containing P•U pairs adjacent to different nearest neighbors. The resulting thermodynamic parameters were compared to RNA duplexes containing A-U pairs in order to determine the contribution of the hydrogen bond involving the exocyclic amino group. Results indicate a loss of 1.78 kcal/mol, on average, when an internal P•U replaces A-U in an RNA duplex. This value is compared to the thermodynamics of a hydrogen bond determined by similar methods. Nearest neighbor parameters were derived for use in free energy and secondary structure prediction software. PMID:28180321

Long-Billed Curlew Breeding Success on Mid-Columbia River National Wildlife Refuges, South-Central Washington and North-Central Oregon, 2007-08

USGS Publications Warehouse

Stocking, Jessica; Elliott-Smith, Elise; Holcomb, Neil; Haig, Susan M.

2010-01-01

Long-billed curlew (Numenius americanus) reproductive success was evaluated on the Mid-Columbia River National Wildlife Refuges of south-central Washington and north-central Oregon during the 2007 and 2008 breeding seasons. Additionally, we assisted the U.S. Fish and Wildlife Service in collecting information on distribution, abundance, and brood habitat for this shorebird species of conservation concern. A total of 32 breeding pairs were located on the refuges in 2007 and 35 pairs were located in 2008. We monitored 17 nests in 2007 and 23 nests in 2008. Curlew pairs were most abundant on Hanford Reach National Monument in 2007 but more nests were located on Umatilla National Wildlife Refuge in both years, with Columbia National Wildlife Refuge supporting few pairs. Nest success was 23.6 percent in 2007 and 32.9 percent in 2008 after taking into account exposure time and combining data for all the refuges. We were unable to detect any relationship between nest success and habitat type or habitat variables measured. However, our study was the first to document use of agricultural fields on the refuge as curlew nest habitat. We collected 39 and 28 brood locations in 2007 and 2008, respectively, and many observations were likely resightings of the same brood. Broods used a similar variety of habitats as nesting curlew and no clear habitat use pattern was detected.

Comparing transverse momentum balance of b jet pairs in pp and PbPb collisions at $$\\sqrt{s_\\mathrm{NN}} =$$ 5.02 TeV

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

Sirunyan, Albert M.

The transverse momentum balance of pairs of back-to-back b quark jets in PbPb and pp collisions recorded with the CMS detector at the LHC is reported. The center-of-mass energy in both collision systems is 5.02 TeV per nucleon pair. Compared to the pp collision baseline, b quark jets have a larger imbalance in the most central PbPb collisions, as expected from the jet quenching effect. The data are also compared to the corresponding measurement with inclusive dijets. In the most central collisions, the imbalance of b quark dijets is comparable to that of inclusive dijets.

Comparing transverse momentum balance of b jet pairs in pp and PbPb collisions at $$\\sqrt{s_\\mathrm{NN}} =$$ 5.02 TeV

DOE PAGES

Sirunyan, Albert M.

2018-03-29

The transverse momentum balance of pairs of back-to-back b quark jets in PbPb and pp collisions recorded with the CMS detector at the LHC is reported. The center-of-mass energy in both collision systems is 5.02 TeV per nucleon pair. Compared to the pp collision baseline, b quark jets have a larger imbalance in the most central PbPb collisions, as expected from the jet quenching effect. The data are also compared to the corresponding measurement with inclusive dijets. In the most central collisions, the imbalance of b quark dijets is comparable to that of inclusive dijets.

A single base pair in the right terminal domain of tomato planta macho viroid is a virulence determinant factor on tomato.

PubMed

Li, Rugang; Padmanabhan, Chellappan; Ling, Kai-Shu

2017-01-01

Tomato planta macho viroid (TPMVd), including isolates previously designated as Mexican papita viroid (MPVd), causes serious disease on tomatoes in North America. Two predominant variants, sharing 93.8% sequence identity, incited distinct severe (MPVd-S) or mild (MPVd-M) symptoms on tomato. To identify virulence determinant factor, a series of chimeric infectious clones were generated using synthetic DNA approach to progressively replace each structural domain between the two variants. In bioassays on tomato 'Rutgers', three chimeras containing Terminal Left and Pathogenicity (MPVd-H1), Central (MPVd-H2), or Variable (MPVd-H3) of MPVd-S, incited mild to intermediate symptoms. However, a chimera containing Terminal Right (T R ) of MPVd-S (MPVd-H4) incited severe symptoms. Only one base-pair mutation in the T R domain between MPVd-M ( 176 U:A 185 ) and MPVd-S ( 174 G:C 183 ) was identified. A reciprocal mutant (MPVd-H5) rendered the chimeric viroid mild on tomato. This single base-pair in the T R domain was determined as the virulence determinant factor for TPMVd. Published by Elsevier Inc.

Transfer of classical eyeblink conditioning with electrical stimulation of mPFC or tone as conditioned stimulus in guinea pigs.

PubMed

Yao, Juan; Wu, Guang-Yan; Liu, Guo-Long; Liu, Shu-Lei; Yang, Yi; Wu, Bing; Li, Xuan; Feng, Hua; Sui, Jian-Feng

2014-11-01

Learning with a stimulus from one sensory modality can facilitate subsequent learning with a new stimulus from a different sensory modality. To date, the characteristics and mechanism of this phenomenon named transfer effect still remain ambiguous. Our previous work showed that electrical stimulation of medial prefrontal cortex (mPFC) as a conditioned stimulus (CS) could successfully establish classical eyeblink conditioning (EBC). The present study aimed to (1) observe whether transfer of EBC learning would occur when CSs shift between central (mPFC electrical stimulation as a CS, mPFC-CS) and peripheral (tone as a CS, tone CS); (2) compare the difference in transfer effect between the two paradigms, delay EBC (DEBC) and trace EBC (TEBC). A total of 8 groups of guinea pigs were tested in the study, including 4 experimental groups and 4 control groups. Firstly, the experimental groups accepted central (or peripheral) CS paired with corneal airpuff unconditioned stimulus (US); then, CS shifted to the peripheral (or central) and paired with US. The control groups accepted corresponding central (or peripheral) CS and pseudo-paired with US, and then shifted CS from central (or peripheral) to peripheral (or central) and paired with US. The results showed that the acquisition rates of EBC were higher in experimental groups than in control groups after CS switching from central to peripheral or vice versa, and the CR acquisition rate was remarkably higher in DEBC than in TEBC in both transfer ways. The results indicate that EBC transfer can occur between learning established with mPFC-CS and tone CS. Memory of CS-US association for delay paradigm was less disturbed by the sudden switch of CS than for trace paradigm. This study provides new insight into neural mechanisms underlying conditioned reflex as well as the role of mPFC. Copyright © 2014 Elsevier B.V. All rights reserved.

Symbol/Meaning Paired-Associate Recall: An “Archetypal Memory” Advantage?

PubMed Central

Sotirova-Kohli, Milena; Opwis, Klaus; Roesler, Christian; Smith, Steven M.; Rosen, David H.; Vaid, Jyotsna; Djonov, Valentin

2013-01-01

The theory of the archetypes and the hypothesis of the collective unconscious are two of the central characteristics of analytical psychology. These provoke, however, varying reactions among academic psychologists. Empirical studies which test these hypotheses are rare. Rosen, Smith, Huston and Gonzales proposed a cognitive psychological experimental paradigm to investigate the nature of archetypes and the collective unconscious as archetypal (evolutionary) memory. In this article we report the results of a cross-cultural replication of Rosen et al. conducted in the German-speaking part of Switzerland. In short, this experiment corroborated previous findings by Rosen et al., based on English speakers, and demonstrated a recall advantage for archetypal symbol meaning pairs vs. other symbol/meaning pairings. The fact that the same pattern of results was observed across two different cultures and languages makes it less likely that they are attributable to a specific cultural or linguistic context. PMID:25379255

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

PubMed

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

2018-01-23

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

Molecular Confirmation of the Specific Status of Anopheles halophylus (Diptera: Culicidae) and Evidence of a New Cryptic Species within An. triannulatus in Central Brazil

DTIC Science & Technology

2006-01-01

unbiased genetic dis- tances and characterized using the unweighted pair group method with arithmetic means ( UPGMA ). Re- Table 1. Gene frequencies for...0.428, and between An. halophylus and the morpho- logical variant was 0.145, supporting the observations seen with allozymes. A UPGMA dendrogram based...and R. C. Wilkerson. 2005. Anopheles tri- annulatus (Neiva and Pinto): a new Anopheles record Fig. 2. UPGMA dendrogram constructed based on RAPD

Peripheral Opioid Analgesia

DTIC Science & Technology

1999-07-16

central nervous system by neurons called primary afferent nociceptors (PANs). These neurons have their cell bodies in the dorsal root ganglia (ORG... neurons , and in particular their role in the generation, propagation and modulation of noxious stimulation will be summarized. The final section of...and processing of each opioid peptide is discussed below. The human POMC gene is 7665 base pairs (bp) long which contains three exons and two

Teaching Valence Shell Electron Pair Repulsion (VSEPR) Theory

ERIC Educational Resources Information Center

Talbot, Christopher; Neo, Choo Tong

2013-01-01

This "Science Note" looks at the way that the shapes of simple molecules can be explained in terms of the number of electron pairs in the valence shell of the central atom. This theory is formally known as valence shell electron pair repulsion (VSEPR) theory. The article explains the preferred shape of chlorine trifluoride (ClF3),…

The First Row Anomaly and Recoupled Pair Bonding in the Halides of the Late p-Block Elements

PubMed Central

2012-01-01

The dramatic differences between the properties of molecules formed from the late p-block elements of the first row of the periodic table (N–F) and those of the corresponding elements in subsequent rows is well recognized as the first row anomaly. Certain properties of the atoms, such as the relative energies and spatial extents of the ns and np orbitals, can explain some of these differences, but not others. In this Account, we summarize the results of our recent computational studies of the halides of the late p-block elements. Our studies point to a single underlying cause for many of these differences: the ability of the late p-block elements in the second and subsequent rows of the periodic table to form recoupled pair bonds and recoupled pair bond dyads with very electronegative ligands. Recoupled pair bonds form when an electron in a singly occupied ligand orbital recouples the pair of electrons in a doubly occupied lone pair orbital on the central atom, leading to a central atom-ligand bond. Recoupled pair bond dyads occur when a second ligand forms a bond with the orbital left over from the initial recoupled pair bond. Recoupled pair bonds and recoupled pair bond dyads enable the late p-block elements to form remarkably stable hypervalent compounds such as PF5 and SF6 and lead to unexpected excited states in smaller halides of the late p-block elements such as SF and SF2. Recoupled pair bonding also causes the Fn–1X–F bond energies to oscillate dramatically once the normal valences of the central atoms have been satisfied. In addition, recoupled pair bonding provides a lower-energy pathway for inversion in heavily fluorinated compounds (PF3 and PF2H, but not PH2F and PH3) and leads to unusual intermediates and products in reactions involving halogens and late p-block element compounds, such as (CH3)2S + F2. Although this Account focuses on the halides of the second row, late p-block elements, recoupled pair bonds and recoupled pair bond dyads are important in the chemistry of p-block elements beyond the second row (As, Se, and Br) and for compounds of these elements with other very electronegative ligands, such as OH and O. Knowledge of recoupled pair bonding is thus critical to understanding the properties and reactivity of molecules containing the late p-block elements beyond the first row. PMID:23151313

The first row anomaly and recoupled pair bonding in the halides of the late p-block elements.

PubMed

Dunning, Thom H; Woon, David E; Leiding, Jeff; Chen, Lina

2013-02-19

The dramatic differences between the properties of molecules formed from the late p-block elements of the first row of the periodic table (N-F) and those of the corresponding elements in subsequent rows is well recognized as the first row anomaly. Certain properties of the atoms, such as the relative energies and spatial extents of the ns and np orbitals, can explain some of these differences, but not others. In this Account, we summarize the results of our recent computational studies of the halides of the late p-block elements. Our studies point to a single underlying cause for many of these differences: the ability of the late p-block elements in the second and subsequent rows of the periodic table to form recoupled pair bonds and recoupled pair bond dyads with very electronegative ligands. Recoupled pair bonds form when an electron in a singly occupied ligand orbital recouples the pair of electrons in a doubly occupied lone pair orbital on the central atom, leading to a central atom-ligand bond. Recoupled pair bond dyads occur when a second ligand forms a bond with the orbital left over from the initial recoupled pair bond. Recoupled pair bonds and recoupled pair bond dyads enable the late p-block elements to form remarkably stable hypervalent compounds such as PF(5) and SF(6) and lead to unexpected excited states in smaller halides of the late p-block elements such as SF and SF(2). Recoupled pair bonding also causes the F(n-1)X-F bond energies to oscillate dramatically once the normal valences of the central atoms have been satisfied. In addition, recoupled pair bonding provides a lower-energy pathway for inversion in heavily fluorinated compounds (PF(3) and PF(2)H, but not PH(2)F and PH(3)) and leads to unusual intermediates and products in reactions involving halogens and late p-block element compounds, such as (CH(3))(2)S + F(2). Although this Account focuses on the halides of the second row, late p-block elements, recoupled pair bonds and recoupled pair bond dyads are important in the chemistry of p-block elements beyond the second row (As, Se, and Br) and for compounds of these elements with other very electronegative ligands, such as OH and O. Knowledge of recoupled pair bonding is thus critical to understanding the properties and reactivity of molecules containing the late p-block elements beyond the first row.

Discovering Implicit Entity Relation with the Gene-Citation-Gene Network

PubMed Central

Song, Min; Han, Nam-Gi; Kim, Yong-Hwan; Ding, Ying; Chambers, Tamy

2013-01-01

In this paper, we apply the entitymetrics model to our constructed Gene-Citation-Gene (GCG) network. Based on the premise there is a hidden, but plausible, relationship between an entity in one article and an entity in its citing article, we constructed a GCG network of gene pairs implicitly connected through citation. We compare the performance of this GCG network to a gene-gene (GG) network constructed over the same corpus but which uses gene pairs explicitly connected through traditional co-occurrence. Using 331,411 MEDLINE abstracts collected from 18,323 seed articles and their references, we identify 25 gene pairs. A comparison of these pairs with interactions found in BioGRID reveal that 96% of the gene pairs in the GCG network have known interactions. We measure network performance using degree, weighted degree, closeness, betweenness centrality and PageRank. Combining all measures, we find the GCG network has more gene pairs, but a lower matching rate than the GG network. However, combining top ranked genes in both networks produces a matching rate of 35.53%. By visualizing both the GG and GCG networks, we find that cancer is the most dominant disease associated with the genes in both networks. Overall, the study indicates that the GCG network can be useful for detecting gene interaction in an implicit manner. PMID:24358368

Species composition of developing Central Appalachian hardwood stands following clearcutting

Treesearch

Lance A. Vickers; Thomas Fox

2015-01-01

This study examined the species composition of 47 paired stands on submesic sites on the Appalachian Plateau of West Virginia. Paired stands consisted of a mature stand adjacent to a young clearcut that was

A Novel Centrality Measure for Network-wide Cyber Vulnerability Assessment

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

Sathanur, Arun V.; Haglin, David J.

In this work we propose a novel formulation that models the attack and compromise on a cyber network as a combination of two parts - direct compromise of a host and the compromise occurring through the spread of the attack on the network from a compromised host. The model parameters for the nodes are a concise representation of the host profiles that can include the risky behaviors of the associated human users while the model parameters for the edges are based on the existence of vulnerabilities between each pair of connected hosts. The edge models relate to the summary representationsmore » of the corresponding attack-graphs. This results in a formulation based on Random Walk with Restart (RWR) and the resulting centrality metric can be solved for in an efficient manner through the use of sparse linear solvers. Thus the formulation goes beyond mere topological considerations in centrality computations by summarizing the host profiles and the attack graphs into the model parameters. The computational efficiency of the method also allows us to also quantify the uncertainty in the centrality measure through Monte Carlo analysis.« less

Search for the Standard Model Higgs Boson in the Diphoton Final State in $$p\\bar{p}$$ Collisions at $$\\sqrt{s}$$ = 1.96 TeV Using the CDF II Detector

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

Bland, Karen Renee

2012-01-01

We present a search for the Standard Model Higgs boson decaying into a pair of photons produced in pmore » $$p\\bar{p}$$ collisions with a center of mass energy of 1.96 TeV. The results are based on data corresponding to an integrated luminosity of 10 fb -1 collected by the CDF II detector. Higgs boson candidate events are identified by reconstructing two photons in either the central or plug regions of the detector. The acceptance for identifying photons is significantly increased by using a new algorithm designed to reconstruct photons in the central region that have converted to an electron-positron pair. In addition, a new neural network discriminant is employed to improve the identification of non-converting central photons. No evidence for the Higgs boson is observed in the data, and we set an upper limit on the cross section for Higgs boson production multiplied by the H → γγ branching ratio. For a Higgs boson mass of 125 GeV/c 2 , we obtain an observed (expected) limit of 12.2 (10.8) times the Standard Model prediction at the 95% credibility level.« less

Diversity of chloroplast genome among local clones of cocoa (Theobroma cacao, L.) from Central Sulawesi

NASA Astrophysics Data System (ADS)

Suwastika, I. Nengah; Pakawaru, Nurul Aisyah; Rifka, Rahmansyah, Muslimin, Ishizaki, Yoko; Cruz, André Freire; Basri, Zainuddin; Shiina, Takashi

2017-02-01

Chloroplast genomes typically range in size from 120 to 170 kilo base pairs (kb), which relatively conserved among plant species. Recent evaluation on several species, certain unique regions showed high variability which can be utilized in the phylogenetic analysis. Many fragments of coding regions, introns, and intergenic spacers, such as atpB-rbcL, ndhF, rbcL, rpl16, trnH-psbA, trnL-F, trnS-G, etc., have been used for phylogenetic reconstructions at various taxonomic levels. Based on that status, we would like to analysis the diversity of chloroplast genome within species of local cacao (Theobroma cacao L.) from Central Sulawesi. Our recent data showed, there were more than 20 clones from local farming in Central Sulawesi, and it can be detected based on phenotypic and nuclear-genome-based characterization (RAPD- Random Amplified Polymorphic DNA and SSR- Simple Sequences Repeat) markers. In developing DNA marker for this local cacao, here we also included analysis based on the variation of chloroplast genome. At least several regions such as rpl32-TurnL, it can be considered as chloroplast markers on our local clone of cocoa. Furthermore, we could develop phylogenetic analysis in between clones of cocoa.

Centromere Pairing in Early Meiotic Prophase Requires Active Centromeres and Precedes Installation of the Synaptonemal Complex in Maize[W

PubMed Central

Zhang, Jing; Pawlowski, Wojciech P.; Han, Fangpu

2013-01-01

Pairing of homologous chromosomes in meiosis is critical for their segregation to daughter cells. In most eukaryotes, clustering of telomeres precedes and facilitates chromosome pairing. In several species, centromeres also form pairwise associations, known as coupling, before the onset of pairing. We found that, in maize (Zea mays), centromere association begins at the leptotene stage and occurs earlier than the formation of the telomere bouquet. We established that centromere pairing requires centromere activity and the sole presence of centromeric repeats is not sufficient for pairing. In several species, homologs of the ZIP1 protein, which forms the central element of the synaptonemal complex in budding yeast (Saccharomyces cerevisiae), play essential roles in centromere coupling. However, we found that the maize ZIP1 homolog ZYP1 installs in the centromeric regions of chromosomes after centromeres form associations. Instead, we found that maize STRUCTURAL MAINTENANCE OF CHROMOSOMES6 homolog forms a central element of the synaptonemal complex, which is required for centromere associations. These data shed light on the poorly understood mechanism of centromere interactions and suggest that this mechanism may vary somewhat in different species. PMID:24143803

Centromere pairing in early meiotic prophase requires active centromeres and precedes installation of the synaptonemal complex in maize.

PubMed

Zhang, Jing; Pawlowski, Wojciech P; Han, Fangpu

2013-10-01

Pairing of homologous chromosomes in meiosis is critical for their segregation to daughter cells. In most eukaryotes, clustering of telomeres precedes and facilitates chromosome pairing. In several species, centromeres also form pairwise associations, known as coupling, before the onset of pairing. We found that, in maize (Zea mays), centromere association begins at the leptotene stage and occurs earlier than the formation of the telomere bouquet. We established that centromere pairing requires centromere activity and the sole presence of centromeric repeats is not sufficient for pairing. In several species, homologs of the ZIP1 protein, which forms the central element of the synaptonemal complex in budding yeast (Saccharomyces cerevisiae), play essential roles in centromere coupling. However, we found that the maize ZIP1 homolog ZYP1 installs in the centromeric regions of chromosomes after centromeres form associations. Instead, we found that maize structural maintenance of chromosomes6 homolog forms a central element of the synaptonemal complex, which is required for centromere associations. These data shed light on the poorly understood mechanism of centromere interactions and suggest that this mechanism may vary somewhat in different species.

Individually adapted imagery improves brain-computer interface performance in end-users with disability.

PubMed

Scherer, Reinhold; Faller, Josef; Friedrich, Elisabeth V C; Opisso, Eloy; Costa, Ursula; Kübler, Andrea; Müller-Putz, Gernot R

2015-01-01

Brain-computer interfaces (BCIs) translate oscillatory electroencephalogram (EEG) patterns into action. Different mental activities modulate spontaneous EEG rhythms in various ways. Non-stationarity and inherent variability of EEG signals, however, make reliable recognition of modulated EEG patterns challenging. Able-bodied individuals who use a BCI for the first time achieve - on average - binary classification performance of about 75%. Performance in users with central nervous system (CNS) tissue damage is typically lower. User training generally enhances reliability of EEG pattern generation and thus also robustness of pattern recognition. In this study, we investigated the impact of mental tasks on binary classification performance in BCI users with central nervous system (CNS) tissue damage such as persons with stroke or spinal cord injury (SCI). Motor imagery (MI), that is the kinesthetic imagination of movement (e.g. squeezing a rubber ball with the right hand), is the "gold standard" and mainly used to modulate EEG patterns. Based on our recent results in able-bodied users, we hypothesized that pair-wise combination of "brain-teaser" (e.g. mental subtraction and mental word association) and "dynamic imagery" (e.g. hand and feet MI) tasks significantly increases classification performance of induced EEG patterns in the selected end-user group. Within-day (How stable is the classification within a day?) and between-day (How well does a model trained on day one perform on unseen data of day two?) analysis of variability of mental task pair classification in nine individuals confirmed the hypothesis. We found that the use of the classical MI task pair hand vs. feed leads to significantly lower classification accuracy - in average up to 15% less - in most users with stroke or SCI. User-specific selection of task pairs was again essential to enhance performance. We expect that the gained evidence will significantly contribute to make imagery-based BCI technology become accessible to a larger population of users including individuals with special needs due to CNS damage.

SU-F-J-205: Effect of Cone Beam Factor On Cone Beam CT Number Accuracy

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

Yao, W; Hua, C; Farr, J

Purpose: To examine the suitability of a Catphan™ 700 phantom for image quality QA of a cone beam computed tomography (CBCT) system deployed for proton therapy. Methods: Catphan phantoms, particularly Catphan™ 504, are commonly used in image quality QA for CBCT. As a newer product, Catphan™ 700 offers more tissue equivalent inserts which may be useful for generating the electron density – CT number curve for CBCT based treatment planning. The sensitometry-and-geometry module used in Catphan™ 700 is located at the end of the phantom and after the resolution line pair module. In Catphan™ 504 the line pair module ismore » located at the end of the phantom and after the sensitometry-and-geometry module. To investigate the effect of difference in location on CT number accuracy due to the cone beam factor, we scanned the Catphan™ 700 with the central plane of CBCT at the center of the phantom, line pair and sensitometry-andgeometry modules of the phantom, respectively. The protocol head and thorax scan modes were used. For each position, scans were repeated 4 times. Results: For the head scan mode, the standard deviation (SD) of the CT numbers of each insert under 4 repeated scans was up to 20 HU, 11 HU, and 11 HU, respectively, for the central plane of CBCT located at the center of the phantom, line pair, and sensitometry-and-geometry modules of the phantom. The mean of the SD was 9.9 HU, 5.7 HU, and 5.9 HU, respectively. For the thorax mode, the mean of the SD was 4.5 HU, 4.4 HU, and 4.4 HU, respectively. The assessment of image quality based on resolution and spatial linearity was not affected by imaging location changes. Conclusion: When the Catphan™ 700 was aligned to the center of imaging region, the CT number accuracy test may not meet expectations. We recommend reconfiguration of the modules.« less

Individually Adapted Imagery Improves Brain-Computer Interface Performance in End-Users with Disability

PubMed Central

Scherer, Reinhold; Faller, Josef; Friedrich, Elisabeth V. C.; Opisso, Eloy; Costa, Ursula; Kübler, Andrea; Müller-Putz, Gernot R.

2015-01-01

Brain-computer interfaces (BCIs) translate oscillatory electroencephalogram (EEG) patterns into action. Different mental activities modulate spontaneous EEG rhythms in various ways. Non-stationarity and inherent variability of EEG signals, however, make reliable recognition of modulated EEG patterns challenging. Able-bodied individuals who use a BCI for the first time achieve - on average - binary classification performance of about 75%. Performance in users with central nervous system (CNS) tissue damage is typically lower. User training generally enhances reliability of EEG pattern generation and thus also robustness of pattern recognition. In this study, we investigated the impact of mental tasks on binary classification performance in BCI users with central nervous system (CNS) tissue damage such as persons with stroke or spinal cord injury (SCI). Motor imagery (MI), that is the kinesthetic imagination of movement (e.g. squeezing a rubber ball with the right hand), is the "gold standard" and mainly used to modulate EEG patterns. Based on our recent results in able-bodied users, we hypothesized that pair-wise combination of "brain-teaser" (e.g. mental subtraction and mental word association) and "dynamic imagery" (e.g. hand and feet MI) tasks significantly increases classification performance of induced EEG patterns in the selected end-user group. Within-day (How stable is the classification within a day?) and between-day (How well does a model trained on day one perform on unseen data of day two?) analysis of variability of mental task pair classification in nine individuals confirmed the hypothesis. We found that the use of the classical MI task pair hand vs. feed leads to significantly lower classification accuracy - in average up to 15% less - in most users with stroke or SCI. User-specific selection of task pairs was again essential to enhance performance. We expect that the gained evidence will significantly contribute to make imagery-based BCI technology become accessible to a larger population of users including individuals with special needs due to CNS damage. PMID:25992718

Comparing transverse momentum balance of b jet pairs in pp and PbPb collisions at √{s_{NN}}=5.02 TeV

NASA Astrophysics Data System (ADS)

Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Ambrogi, F.; Asilar, E.; Bergauer, T.; Brandstetter, J.; Brondolin, E.; Dragicevic, M.; Erö, J.; Escalante Del Valle, A.; Flechl, M.; Friedl, M.; Frühwirth, R.; Ghete, V. M.; Grossmann, J.; Hrubec, J.; Jeitler, M.; König, A.; Krammer, N.; Krätschmer, I.; Liko, D.; Madlener, T.; Mikulec, I.; Pree, E.; Rad, N.; Rohringer, H.; Schieck, J.; Schöfbeck, R.; Spanring, M.; Spitzbart, D.; Taurok, A.; Waltenberger, W.; Wittmann, J.; Wulz, C.-E.; Zarucki, M.; Chekhovsky, V.; Mossolov, V.; Suarez Gonzalez, J.; De Wolf, E. A.; Di Croce, D.; Janssen, X.; Lauwers, J.; Pieters, M.; Van De Klundert, M.; Van Haevermaet, H.; Van Mechelen, P.; Van Remortel, N.; Abu Zeid, S.; Blekman, F.; D'Hondt, J.; De Bruyn, I.; De Clercq, J.; Deroover, K.; Flouris, G.; Lontkovskyi, D.; Lowette, S.; Marchesini, I.; Moortgat, S.; Moreels, L.; Python, Q.; Skovpen, K.; Tavernier, S.; Van Doninck, W.; Van Mulders, P.; Van Parijs, I.; Beghin, D.; Bilin, B.; Brun, H.; Clerbaux, B.; De Lentdecker, G.; Delannoy, H.; Dorney, B.; Fasanella, G.; Favart, L.; Goldouzian, R.; Grebenyuk, A.; Kalsi, A. K.; Lenzi, T.; Luetic, J.; Seva, T.; Starling, E.; Vander Velde, C.; Vanlaer, P.; Vannerom, D.; Yonamine, R.; Cornelis, T.; Dobur, D.; Fagot, A.; Gul, M.; Khvastunov, I.; Poyraz, D.; Roskas, C.; Trocino, D.; Tytgat, M.; Verbeke, W.; Vermassen, B.; Vit, M.; Zaganidis, N.; Bakhshiansohi, H.; Bondu, O.; Brochet, S.; Bruno, G.; Caputo, C.; Caudron, A.; David, P.; De Visscher, S.; Delaere, C.; Delcourt, M.; Francois, B.; Giammanco, A.; Krintiras, G.; Lemaitre, V.; Magitteri, A.; Mertens, A.; Musich, M.; Piotrzkowski, K.; Quertenmont, L.; Saggio, A.; Vidal Marono, M.; Wertz, S.; Zobec, J.; Aldá Júnior, W. L.; Alves, F. L.; Alves, G. A.; Brito, L.; Correia Silva, G.; Hensel, C.; Moraes, A.; Pol, M. E.; Rebello Teles, P.; Belchior Batista Das Chagas, E.; Carvalho, W.; Chinellato, J.; Coelho, E.; Da Costa, E. M.; Da Silveira, G. G.; De Jesus Damiao, D.; Fonseca De Souza, S.; Malbouisson, H.; Medina Jaime, M.; Melo De Almeida, M.; Mora Herrera, C.; Mundim, L.; Nogima, H.; Sanchez Rosas, L. J.; Santoro, A.; Sznajder, A.; Thiel, M.; Tonelli Manganote, E. J.; Torres Da Silva De Araujo, F.; Vilela Pereira, A.; Ahuja, S.; Bernardes, C. A.; Calligaris, L.; Fernandez Perez Tomei, T. R.; Gregores, E. M.; Mercadante, P. G.; Novaes, S. F.; Padula, Sandra S.; Romero Abad, D.; Ruiz Vargas, J. C.; Aleksandrov, A.; Hadjiiska, R.; Iaydjiev, P.; Marinov, A.; Misheva, M.; Rodozov, M.; Shopova, M.; Sultanov, G.; Dimitrov, A.; Litov, L.; Pavlov, B.; Petkov, P.; Fang, W.; Gao, X.; Yuan, L.; Ahmad, M.; Bian, J. G.; Chen, G. M.; Chen, H. S.; Chen, M.; Chen, Y.; Jiang, C. H.; Leggat, D.; Liao, H.; Liu, Z.; Romeo, F.; Shaheen, S. M.; Spiezia, A.; Tao, J.; Wang, C.; Wang, Z.; Yazgan, E.; Zhang, H.; Zhao, J.; Ban, Y.; Chen, G.; Li, J.; Li, Q.; Liu, S.; Mao, Y.; Qian, S. J.; Wang, D.; Xu, Z.; Wang, Y.; Avila, C.; Cabrera, A.; Carrillo Montoya, C. A.; Chaparro Sierra, L. F.; Florez, C.; González Hernández, C. F.; Segura Delgado, M. A.; Courbon, B.; Godinovic, N.; Lelas, D.; Puljak, I.; Ribeiro Cipriano, P. M.; Sculac, T.; Antunovic, Z.; Kovac, M.; Brigljevic, V.; Ferencek, D.; Kadija, K.; Mesic, B.; Starodumov, A.; Susa, T.; Ather, M. W.; Attikis, A.; Mavromanolakis, G.; Mousa, J.; Nicolaou, C.; Ptochos, F.; Razis, P. A.; Rykaczewski, H.; Finger, M.; Finger, M.; Carrera Jarrin, E.; Abdalla, H.; Mahmoud, M. A.; Mohammed, Y.; Bhowmik, S.; Dewanjee, R. K.; Kadastik, M.; Perrini, L.; Raidal, M.; Veelken, C.; Eerola, P.; Kirschenmann, H.; Pekkanen, J.; Voutilainen, M.; Havukainen, J.; Heikkilä, J. K.; Järvinen, T.; Karimäki, V.; Kinnunen, R.; Lampén, T.; Lassila-Perini, K.; Laurila, S.; Lehti, S.; Lindén, T.; Luukka, P.; Mäenpää, T.; Siikonen, H.; Tuominen, E.; Tuominiemi, J.; Tuuva, T.; Besancon, M.; Couderc, F.; Dejardin, M.; Denegri, D.; Faure, J. 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M.; Rabady, D.; Racz, A.; Reis, T.; Rolandi, G.; Rovere, M.; Sakulin, H.; Schäfer, C.; Schwick, C.; Seidel, M.; Selvaggi, M.; Sharma, A.; Silva, P.; Sphicas, P.; Stakia, A.; Steggemann, J.; Stoye, M.; Tosi, M.; Treille, D.; Tsirou, A.; Veckalns, V.; Verweij, M.; Zeuner, W. D.; Bertl, W.; Caminada, L.; Deiters, K.; Erdmann, W.; Horisberger, R.; Ingram, Q.; Kaestli, H. C.; Kotlinski, D.; Langenegger, U.; Rohe, T.; Wiederkehr, S. A.; Backhaus, M.; Bäni, L.; Berger, P.; Casal, B.; Chernyavskaya, N.; Dissertori, G.; Dittmar, M.; Donegà, M.; Dorfer, C.; Grab, C.; Heidegger, C.; Hits, D.; Hoss, J.; Klijnsma, T.; Lustermann, W.; Marionneau, M.; Meinhard, M. T.; Meister, D.; Micheli, F.; Musella, P.; NessiTedaldi, F.; Pata, J.; Pauss, F.; Perrin, G.; Perrozzi, L.; Quittnat, M.; Reichmann, M.; Ruini, D.; Sanz Becerra, D. A.; Schönenberger, M.; Shchutska, L.; Tavolaro, V. R.; Theofilatos, K.; Vesterbacka Olsson, M. L.; Wallny, R.; Zhu, D. H.; Aarrestad, T. K.; Amsler, C.; Brzhechko, D.; Canelli, M. F.; De Cosa, A.; Del Burgo, R.; Donato, S.; Galloni, C.; Hreus, T.; Kilminster, B.; Neutelings, I.; Pinna, D.; Rauco, G.; Robmann, P.; Salerno, D.; Schweiger, K.; Seitz, C.; Takahashi, Y.; Zucchetta, A.; Candelise, V.; Chang, Y. H.; Cheng, K. y.; Doan, T. H.; Jain, Sh.; Khurana, R.; Kuo, C. M.; Lin, W.; Pozdnyakov, A.; Yu, S. S.; Kumar, Arun; Chang, P.; Chao, Y.; Chen, K. F.; Chen, P. H.; Fiori, F.; Hou, W.-S.; Hsiung, Y.; Liu, Y. F.; Lu, R.-S.; Paganis, E.; Psallidas, A.; Steen, A.; Tsai, J. f.; Asavapibhop, B.; Kovitanggoon, K.; Singh, G.; Srimanobhas, N.; Bat, A.; Boran, F.; Cerci, S.; Damarseckin, S.; Demiroglu, Z. S.; Dozen, C.; Dumanoglu, I.; Girgis, S.; Gokbulut, G.; Guler, Y.; Hos, I.; Kangal, E. E.; Kara, O.; Kayis Topaksu, A.; Kiminsu, U.; Oglakci, M.; Onengut, G.; Ozdemir, K.; Sunar Cerci, D.; Tok, U. G.; Topakli, H.; Turkcapar, S.; Zorbakir, I. S.; Zorbilmez, C.; Karapinar, G.; Ocalan, K.; Yalvac, M.; Zeyrek, M.; Gülmez, E.; Kaya, M.; Kaya, O.; Tekten, S.; Yetkin, E. A.; Agaras, M. N.; Atay, S.; Cakir, A.; Cankocak, K.; Komurcu, Y.; Grynyov, B.; Levchuk, L.; Ball, F.; Beck, L.; Brooke, J. J.; Burns, D.; Clement, E.; Cussans, D.; Davignon, O.; Flacher, H.; Goldstein, J.; Heath, G. P.; Heath, H. F.; Kreczko, L.; Newbold, D. M.; Paramesvaran, S.; Sakuma, T.; Seif El Nasr-storey, S.; Smith, D.; Smith, V. J.; Belyaev, A.; Brew, C.; Brown, R. M.; Cieri, D.; Cockerill, D. J. A.; Coughlan, J. A.; Harder, K.; Harper, S.; Linacre, J.; Olaiya, E.; Petyt, D.; Shepherd-Themistocleous, C. H.; Thea, A.; Tomalin, I. R.; Williams, T.; Womersley, W. J.; Auzinger, G.; Bainbridge, R.; Bloch, P.; Borg, J.; Breeze, S.; Buchmuller, O.; Bundock, A.; Casasso, S.; Colling, D.; Corpe, L.; Dauncey, P.; Davies, G.; Della Negra, M.; Di Maria, R.; Elwood, A.; Haddad, Y.; Hall, G.; Iles, G.; James, T.; Komm, M.; Lane, R.; Laner, C.; Lyons, L.; Magnan, A.-M.; Malik, S.; Mastrolorenzo, L.; Matsushita, T.; Nash, J.; Nikitenko, A.; Palladino, V.; Pesaresi, M.; Richards, A.; Rose, A.; Scott, E.; Seez, C.; Shtipliyski, A.; Strebler, T.; Summers, S.; Tapper, A.; Uchida, K.; Vazquez Acosta, M.; Virdee, T.; Wardle, N.; Winterbottom, D.; Wright, J.; Zenz, S. C.; Cole, J. E.; Hobson, P. R.; Khan, A.; Kyberd, P.; Morton, A.; Reid, I. D.; Teodorescu, L.; Zahid, S.; Borzou, A.; Call, K.; Dittmann, J.; Hatakeyama, K.; Liu, H.; Pastika, N.; Smith, C.; Bartek, R.; Dominguez, A.; Buccilli, A.; Cooper, S. I.; Henderson, C.; Rumerio, P.; West, C.; Arcaro, D.; Avetisyan, A.; Bose, T.; Gastler, D.; Rankin, D.; Richardson, C.; Rohlf, J.; Sulak, L.; Zou, D.; Benelli, G.; Cutts, D.; Hadley, M.; Hakala, J.; Heintz, U.; Hogan, J. M.; Kwok, K. H. M.; Laird, E.; Landsberg, G.; Lee, J.; Mao, Z.; Narain, M.; Pazzini, J.; Piperov, S.; Sagir, S.; Syarif, R.; Yu, D.; Band, R.; Brainerd, C.; Breedon, R.; Burns, D.; Calderon De La Barca Sanchez, M.; Chertok, M.; Conway, J.; Conway, R.; Cox, P. T.; Erbacher, R.; Flores, C.; Funk, G.; Ko, W.; Lander, R.; Mclean, C.; Mulhearn, M.; Pellett, D.; Pilot, J.; Shalhout, S.; Shi, M.; Smith, J.; Stolp, D.; Taylor, D.; Tos, K.; Tripathi, M.; Wang, Z.; Zhang, F.; Bachtis, M.; Bravo, C.; Cousins, R.; Dasgupta, A.; Florent, A.; Hauser, J.; Ignatenko, M.; Mccoll, N.; Regnard, S.; Saltzberg, D.; Schnaible, C.; Valuev, V.; Bouvier, E.; Burt, K.; Clare, R.; Ellison, J.; Gary, J. W.; Ghiasi Shirazi, S. M. A.; Hanson, G.; Karapostoli, G.; Kennedy, E.; Lacroix, F.; Long, O. R.; Olmedo Negrete, M.; Paneva, M. I.; Si, W.; Wang, L.; Wei, H.; Wimpenny, S.; Yates, B. R.; Branson, J. G.; Cittolin, S.; Derdzinski, M.; Gerosa, R.; Gilbert, D.; Hashemi, B.; Holzner, A.; Klein, D.; Kole, G.; Krutelyov, V.; Letts, J.; Masciovecchio, M.; Olivito, D.; Padhi, S.; Pieri, M.; Sani, M.; Sharma, V.; Simon, S.; Tadel, M.; Vartak, A.; Wasserbaech, S.; Wood, J.; Würthwein, F.; Yagil, A.; Zevi Della Porta, G.; Amin, N.; Bhandari, R.; Bradmiller-Feld, J.; Campagnari, C.; Citron, M.; Dishaw, A.; Dutta, V.; Franco Sevilla, M.; Gouskos, L.; Heller, R.; Incandela, J.; Ovcharova, A.; Qu, H.; Richman, J.; Stuart, D.; Suarez, I.; Yoo, J.; Anderson, D.; Bornheim, A.; Bunn, J.; Lawhorn, J. M.; Newman, H. B.; Nguyen, T. Q.; Pena, C.; Spiropulu, M.; Vlimant, J. R.; Wilkinson, R.; Xie, S.; Zhang, Z.; Zhu, R. Y.; Andrews, M. B.; Ferguson, T.; Mudholkar, T.; Paulini, M.; Russ, J.; Sun, M.; Vogel, H.; Vorobiev, I.; Weinberg, M.; Cumalat, J. P.; Ford, W. T.; Jensen, F.; Johnson, A.; Krohn, M.; Leontsinis, S.; MacDonald, E.; Mulholland, T.; Stenson, K.; Ulmer, K. A.; Wagner, S. R.; Alexander, J.; Chaves, J.; Cheng, Y.; Chu, J.; Datta, A.; Mcdermott, K.; Mirman, N.; Patterson, J. R.; Quach, D.; Rinkevicius, A.; Ryd, A.; Skinnari, L.; Soffi, L.; Tan, S. M.; Tao, Z.; Thom, J.; Tucker, J.; Wittich, P.; Zientek, M.; Abdullin, S.; Albrow, M.; Alyari, M.; Apollinari, G.; Apresyan, A.; Apyan, A.; Banerjee, S.; Bauerdick, L. A. T.; Beretvas, A.; Berryhill, J.; Bhat, P. C.; Bolla, G.; Burkett, K.; Butler, J. N.; Canepa, A.; Cerati, G. B.; Cheung, H. W. K.; Chlebana, F.; Cremonesi, M.; Duarte, J.; Elvira, V. D.; Freeman, J.; Gecse, Z.; Gottschalk, E.; Gray, L.; Green, D.; Grünendahl, S.; Gutsche, O.; Hanlon, J.; Harris, R. M.; Hasegawa, S.; Hirschauer, J.; Hu, Z.; Jayatilaka, B.; Jindariani, S.; Johnson, M.; Joshi, U.; Klima, B.; Kortelainen, M. J.; Kreis, B.; Lammel, S.; Lincoln, D.; Lipton, R.; Liu, M.; Liu, T.; Lopes De Sá, R.; Lykken, J.; Maeshima, K.; Magini, N.; Marraffino, J. M.; Mason, D.; McBride, P.; Merkel, P.; Mrenna, S.; Nahn, S.; O'Dell, V.; Pedro, K.; Prokofyev, O.; Rakness, G.; Ristori, L.; Savoy-Navarro, A.; Schneider, B.; Sexton-Kennedy, E.; Soha, A.; Spalding, W. J.; Spiegel, L.; Stoynev, S.; Strait, J.; Strobbe, N.; Taylor, L.; Tkaczyk, S.; Tran, N. V.; Uplegger, L.; Vaandering, E. W.; Vernieri, C.; Verzocchi, M.; Vidal, R.; Wang, M.; Weber, H. A.; Whitbeck, A.; Wu, W.; Acosta, D.; Avery, P.; Bortignon, P.; Bourilkov, D.; Brinkerhoff, A.; Carnes, A.; Carver, M.; Curry, D.; Field, R. D.; Furic, I. K.; Gleyzer, S. V.; Joshi, B. M.; Konigsberg, J.; Korytov, A.; Kotov, K.; Ma, P.; Matchev, K.; Mei, H.; Mitselmakher, G.; Shi, K.; Sperka, D.; Terentyev, N.; Thomas, L.; Wang, J.; Wang, S.; Yelton, J.; Joshi, Y. R.; Linn, S.; Markowitz, P.; Rodriguez, J. L.; Ackert, A.; Adams, T.; Askew, A.; Hagopian, S.; Hagopian, V.; Johnson, K. F.; Kolberg, T.; Martinez, G.; Perry, T.; Prosper, H.; Saha, A.; Santra, A.; Sharma, V.; Yohay, R.; Baarmand, M. M.; Bhopatkar, V.; Colafranceschi, S.; Hohlmann, M.; Noonan, D.; Roy, T.; Yumiceva, F.; Adams, M. R.; Apanasevich, L.; Berry, D.; Betts, R. R.; Cavanaugh, R.; Chen, X.; Dittmer, S.; Evdokimov, O.; Gerber, C. E.; Hangal, D. A.; Hofman, D. J.; Jung, K.; Kamin, J.; Sandoval Gonzalez, I. D.; Tonjes, M. B.; Varelas, N.; Wang, H.; Wu, Z.; Zhang, J.; Bilki, B.; Clarida, W.; Dilsiz, K.; Durgut, S.; Gandrajula, R. P.; Haytmyradov, M.; Khristenko, V.; Merlo, J.-P.; Mermerkaya, H.; Mestvirishvili, A.; Moeller, A.; Nachtman, J.; Ogul, H.; Onel, Y.; Ozok, F.; Penzo, A.; Snyder, C.; Tiras, E.; Wetzel, J.; Yi, K.; Blumenfeld, B.; Cocoros, A.; Eminizer, N.; Fehling, D.; Feng, L.; Gritsan, A. V.; Maksimovic, P.; Roskes, J.; Sarica, U.; Swartz, M.; Xiao, M.; You, C.; Al-bataineh, A.; Baringer, P.; Bean, A.; Boren, S.; Bowen, J.; Castle, J.; Khalil, S.; Kropivnit-skaya, A.; Majumder, D.; Mcbrayer, W.; Murray, M.; Rogan, C.; Royon, C.; Sanders, S.; Schmitz, E.; Tapia Takaki, J. D.; Wang, Q.; Ivanov, A.; Kaadze, K.; Maravin, Y.; Modak, A.; Mohammadi, A.; Saini, L. K.; Skhirtladze, N.; Rebassoo, F.; Wright, D.; Baden, A.; Baron, O.; Belloni, A.; Eno, S. C.; Feng, Y.; Ferraioli, C.; Hadley, N. J.; Jabeen, S.; Jeng, G. Y.; Kellogg, R. G.; Kunkle, J.; Mignerey, A. C.; Ricci-Tam, F.; Shin, Y. H.; Skuja, A.; Tonwar, S. C.; Abercrombie, D.; Allen, B.; Azzolini, V.; Barbieri, R.; Baty, A.; Bauer, G.; Bi, R.; Brandt, S.; Busza, W.; Cali, I. A.; D'Alfonso, M.; Demiragli, Z.; Gomez Ceballos, G.; Goncharov, M.; Harris, P.; Hsu, D.; Hu, M.; Iiyama, Y.; Innocenti, G. M.; Klute, M.; Kovalskyi, D.; Lee, Y.-J.; Levin, A.; Luckey, P. D.; Maier, B.; Marini, A. C.; Mcginn, C.; Mironov, C.; Narayanan, S.; Niu, X.; Paus, C.; Roland, C.; Roland, G.; Stephans, G. S. F.; Sumorok, K.; Tatar, K.; Velicanu, D.; Wang, J.; Wang, T. W.; Wyslouch, B.; Zhaozhong, S.; Benvenuti, A. C.; Chatterjee, R. M.; Evans, A.; Hansen, P.; Kalafut, S.; Kubota, Y.; Lesko, Z.; Mans, J.; Nourbakhsh, S.; Ruckstuhl, N.; Rusack, R.; Turkewitz, J.; Wadud, M. A.; Acosta, J. G.; Oliveros, S.; Avdeeva, E.; Bloom, K.; Claes, D. R.; Fangmeier, C.; Golf, F.; Gonzalez Suarez, R.; Kamalieddin, R.; Kravchenko, I.; Monroy, J.; Siado, J. E.; Snow, G. R.; Stieger, B.; Godshalk, A.; Harrington, C.; Iashvili, I.; Nguyen, D.; Parker, A.; Rappoccio, S.; Roozbahani, B.; Alverson, G.; Barberis, E.; Freer, C.; Hortiangtham, A.; Massironi, A.; Morse, D. M.; Orimoto, T.; Teixeira De Lima, R.; Wamorkar, T.; Wang, B.; Wisecarver, A.; Wood, D.; Bhattacharya, S.; Charaf, O.; Hahn, K. A.; Mucia, N.; Odell, N.; Schmitt, M. H.; Sung, K.; Trovato, M.; Velasco, M.; Bucci, R.; Dev, N.; Hildreth, M.; Hurtado Anampa, K.; Jessop, C.; Karmgard, D. J.; Kellams, N.; Lannon, K.; Li, W.; Loukas, N.; Marinelli, N.; Meng, F.; Mueller, C.; Musienko, Y.; Planer, M.; Reinsvold, A.; Ruchti, R.; Siddireddy, P.; Smith, G.; Taroni, S.; Wayne, M.; Wightman, A.; Wolf, M.; Woodard, A.; Alimena, J.; Antonelli, L.; Bylsma, B.; Durkin, L. S.; Flowers, S.; Francis, B.; Hart, A.; Hill, C.; Ji, W.; Ling, T. Y.; Luo, W.; Winer, B. L.; Wulsin, H. W.; Cooperstein, S.; Driga, O.; Elmer, P.; Hardenbrook, J.; Hebda, P.; Higginbotham, S.; Kalogeropoulos, A.; Lange, D.; Luo, J.; Marlow, D.; Mei, K.; Ojalvo, I.; Olsen, J.; Palmer, C.; Piroué, P.; Salfeld-Nebgen, J.; Stickland, D.; Tully, C.; Malik, S.; Norberg, S.; Barker, A.; Barnes, V. E.; Das, S.; Gutay, L.; Jones, M.; Jung, A. W.; Khatiwada, A.; Miller, D. H.; Neumeister, N.; Peng, C. C.; Qiu, H.; Schulte, J. F.; Sun, J.; Wang, F.; Xiao, R.; Xie, W.; Cheng, T.; Dolen, J.; Parashar, N.; Chen, Z.; Ecklund, K. M.; Freed, S.; Geurts, F. J. M.; Guilbaud, M.; Kilpatrick, M.; Li, W.; Michlin, B.; Padley, B. P.; Roberts, J.; Rorie, J.; Shi, W.; Tu, Z.; Zabel, J.; Zhang, A.; Bodek, A.; de Barbaro, P.; Demina, R.; Duh, Y. t.; Ferbel, T.; Galanti, M.; Garcia-Bellido, A.; Han, J.; Hindrichs, O.; Khukhunaishvili, A.; Lo, K. H.; Tan, P.; Verzetti, M.; Ciesielski, R.; Goulianos, K.; Mesropian, C.; Agapitos, A.; Chou, J. P.; Gershtein, Y.; Gómez Espinosa, T. A.; Halkiadakis, E.; Heindl, M.; Hughes, E.; Kaplan, S.; Kunnawalkam Elayavalli, R.; Kyriacou, S.; Lath, A.; Montalvo, R.; Nash, K.; Osherson, M.; Saka, H.; Salur, S.; Schnetzer, S.; Sheffield, D.; Somalwar, S.; Stone, R.; Thomas, S.; Thomassen, P.; Walker, M.; Delannoy, A. G.; Heideman, J.; Riley, G.; Rose, K.; Spanier, S.; Thapa, K.; Bouhali, O.; Castaneda Hernandez, A.; Celik, A.; Dalchenko, M.; De Mattia, M.; Delgado, A.; Dildick, S.; Eusebi, R.; Gilmore, J.; Huang, T.; Kamon, T.; Mueller, R.; Pakhotin, Y.; Patel, R.; Perloff, A.; Perniè, L.; Rathjens, D.; Safonov, A.; Tatarinov, A.; Akchurin, N.; Damgov, J.; De Guio, F.; Dudero, P. R.; Faulkner, J.; Gurpinar, E.; Kunori, S.; Lamichhane, K.; Lee, S. W.; Mengke, T.; Muthumuni, S.; Peltola, T.; Undleeb, S.; Volobouev, I.; Wang, Z.; Greene, S.; Gurrola, A.; Janjam, R.; Johns, W.; Maguire, C.; Melo, A.; Ni, H.; Padeken, K.; Ruiz Alvarez, J. D.; Sheldon, P.; Tuo, S.; Velkovska, J.; Xu, Q.; Arenton, M. W.; Barria, P.; Cox, B.; Hirosky, R.; Joyce, M.; Ledovskoy, A.; Li, H.; Neu, C.; Sinthuprasith, T.; Wang, Y.; Wolfe, E.; Xia, F.; Harr, R.; Karchin, P. E.; Poudyal, N.; Sturdy, J.; Thapa, P.; Zaleski, S.; Brodski, M.; Buchanan, J.; Caillol, C.; Carlsmith, D.; Dasu, S.; Dodd, L.; Duric, S.; Gomber, B.; Grothe, M.; Herndon, M.; Hervé, A.; Hussain, U.; Klabbers, P.; Lanaro, A.; Levine, A.; Long, K.; Loveless, R.; Rekovic, V.; Ruggles, T.; Savin, A.; Smith, N.; Smith, W. H.; Woods, N.

2018-03-01

The transverse momentum balance of pairs of back-to-back b quark jets in PbPb and pp collisions recorded with the CMS detector at the LHC is reported. The center-of-mass energy in both collision systems is 5.02 TeV per nucleon pair. Compared to the pp collision baseline, b quark jets have a larger imbalance in the most central PbPb collisions, as expected from the jet quenching effect. The data are also compared to the corresponding measurement with inclusive dijets. In the most central collisions, the imbalance of b quark dijets is comparable to that of inclusive dijets. [Figure not available: see fulltext.

Combined CRISPRi/a-Based Chemical Genetic Screens Reveal that Rigosertib Is a Microtubule-Destabilizing Agent. | Office of Cancer Genomics

Cancer.gov

Chemical libraries paired with phenotypic screens can now readily identify compounds with therapeutic potential. A central limitation to exploiting these compounds, however, has been in identifying their relevant cellular targets. Here, we present a two-tiered CRISPR-mediated chemical-genetic strategy for target identification: combined genome-wide knockdown and overexpression screening as well as focused, comparative chemical-genetic profiling.

γ-Tubulin complex in Trypanosoma brucei: molecular composition, subunit interdependence and requirement for axonemal central pair protein assembly.

PubMed

Zhou, Qing; Li, Ziyin

2015-11-01

γ-Tubulin complex constitutes a key component of the microtubule-organizing center and nucleates microtubule assembly. This complex differs in complexity in different organisms: the budding yeast contains the γ-tubulin small complex (γTuSC) composed of γ-tubulin, gamma-tubulin complex protein (GCP)2 and GCP3, whereas animals contain the γ-tubulin ring complex (γTuRC) composed of γTuSC and three additional proteins, GCP4, GCP5 and GCP6. In Trypanosoma brucei, the composition of the γ-tubulin complex remains elusive, and it is not known whether it also regulates assembly of the subpellicular microtubules and the spindle microtubules. Here we report that the γ-tubulin complex in T. brucei is composed of γ-tubulin and three GCP proteins, GCP2-GCP4, and is primarily localized in the basal body throughout the cell cycle. Depletion of GCP2 and GCP3, but not GCP4, disrupted the axonemal central pair microtubules, but not the subpellicular microtubules and the spindle microtubules. Furthermore, we showed that the γTuSC is required for assembly of two central pair proteins and that γTuSC subunits are mutually required for stability. Together, these results identified an unusual γ-tubulin complex in T. brucei, uncovered an essential role of γTuSC in central pair protein assembly, and demonstrated the interdependence of individual γTuSC components for maintaining a stable complex. © 2015 John Wiley & Sons Ltd.

The γ-tubulin complex in Trypanosoma brucei: molecular composition, subunit interdependence and requirement for axonemal central pair protein assembly

PubMed Central

Zhou, Qing; Li, Ziyin

2015-01-01

The γ-tubulin complex constitutes a key component of the microtubule-organizing center and nucleates microtubule assembly. This complex differs in complexity in different organisms: the budding yeast contains the γ-tubulin small complex (γTuSC) composed of γ-tubulin, GCP2 and GCP3, whereas animals contain the γ-tubulin ring complex (γTuRC) composed of γTuSC and three additional proteins, GCP4, GCP5 and GCP6. In Trypanosoma brucei, the composition of the γ-tubulin complex remains elusive, and it is not known whether it also regulates assembly of the subpellicular microtubules and the spindle microtubules. Here we report that the γ-tubulin complex in T. brucei is composed of γ-tubulin and three GCP proteins, GCP2-GCP4, and is primarily localized in the basal body throughout the cell cycle. Depletion of GCP2 and GCP3, but not GCP4, disrupted the axonemal central pair microtubules, but not the subpellicular microtubules and the spindle microtubules. Furthermore, we showed that the γTuSC is required for assembly of two central pair proteins and that γTuSC subunits are mutually required for stability. Together, these results identified an unusual γ-tubulin complex in T. brucei, uncovered an essential role of γTuSC in central pair protein assembly, and demonstrated the interdependence of individual γTuSC components for maintaining a stable complex. PMID:26224545

Different Roles for Honey Bee Mushroom Bodies and Central Complex in Visual Learning of Colored Lights in an Aversive Conditioning Assay

PubMed Central

Plath, Jenny A.; Entler, Brian V.; Kirkerud, Nicholas H.; Schlegel, Ulrike; Galizia, C. Giovanni; Barron, Andrew B.

2017-01-01

The honey bee is an excellent visual learner, but we know little about how and why it performs so well, or how visual information is learned by the bee brain. Here we examined the different roles of two key integrative regions of the brain in visual learning: the mushroom bodies and the central complex. We tested bees' learning performance in a new assay of color learning that used electric shock as punishment. In this assay a light field was paired with electric shock. The other half of the conditioning chamber was illuminated with light of a different wavelength and not paired with shocks. The unrestrained bee could run away from the light stimulus and thereby associate one wavelength with punishment, and the other with safety. We compared learning performance of bees in which either the central complex or mushroom bodies had been transiently inactivated by microinjection of the reversible anesthetic procaine. Control bees learned to escape the shock-paired light field and to spend more time in the safe light field after a few trials. When ventral lobe neurons of the mushroom bodies were silenced, bees were no longer able to associate one light field with shock. By contrast, silencing of one collar region of the mushroom body calyx did not alter behavior in the learning assay in comparison to control treatment. Bees with silenced central complex neurons did not leave the shock-paired light field in the middle trials of training, even after a few seconds of being shocked. We discussed how mushroom bodies and the central complex both contribute to aversive visual learning with an operant component. PMID:28611605

Pair Housing of Dairy Calves and Age at Pairing: Effects on Weaning Stress, Health, Production and Social Networks.

PubMed

Bolt, Sarah L; Boyland, Natasha K; Mlynski, David T; James, Richard; Croft, Darren P

2017-01-01

The early social environment can influence the health and behaviour of animals, with effects lasting into adulthood. In Europe, around 60% of dairy calves are reared individually during their first eight weeks of life, while others may be housed in pairs or small groups. This study assessed the effects of varying degrees of social contact on weaning stress, health and production during pen rearing, and on the social networks that calves later formed when grouped. Forty female Holstein-Friesian calves were allocated to one of three treatments: individually housed (I, n = 8), pair-housed from day five (P5, n = 8 pairs), and pair-housed from day 28 (P28, n = 8 pairs). From day 48, calves were weaned by gradual reduction of milk over three days, and vocalisations were recorded as a measure of stress for three days before, during and after weaning. Health and production (growth rate and concentrate intakes) were not affected by treatment during the weaning period or over the whole study. Vocalisations were highest post-weaning, and were significantly higher in I calves than pair-reared calves. Furthermore, P28 calves vocalised significantly more than P5 calves. The social network of calves was measured for one month after all calves were grouped in a barn, using association data from spatial proximity loggers. We tested for week-week stability, social differentiation and assortment in the calf network. Additionally, we tested for treatment differences in: coefficient of variation (CV) in association strength, percentage of time spent with ex-penmate (P5 and P28 calves only) and weighted degree centrality (the sum of the strength of an individual's associations). The network was relatively stable from weeks one to four and was significantly differentiated, with individuals assorting based on prior familiarity. P5 calves had significantly higher CV in association strength than I calves in week one (indicating more heterogeneous social associations) but there were no significant treatment differences in week four. The mean percentage of time that individuals spent with their ex-penmate after regrouping decreased from weeks 1-4, though treatment did not affect this. There were also no significant differences in weighted degree centrality between calves in each rearing treatment. These results suggest that early pair-rearing can allow calves the stress buffering benefits of social support (and that this is more effective when calves are paired earlier) without compromising health or production, and sheds light on the early development of social behaviour in cattle.

Pair Housing of Dairy Calves and Age at Pairing: Effects on Weaning Stress, Health, Production and Social Networks

PubMed Central

Mlynski, David T.; James, Richard; Croft, Darren P.

2017-01-01

The early social environment can influence the health and behaviour of animals, with effects lasting into adulthood. In Europe, around 60% of dairy calves are reared individually during their first eight weeks of life, while others may be housed in pairs or small groups. This study assessed the effects of varying degrees of social contact on weaning stress, health and production during pen rearing, and on the social networks that calves later formed when grouped. Forty female Holstein-Friesian calves were allocated to one of three treatments: individually housed (I, n = 8), pair-housed from day five (P5, n = 8 pairs), and pair-housed from day 28 (P28, n = 8 pairs). From day 48, calves were weaned by gradual reduction of milk over three days, and vocalisations were recorded as a measure of stress for three days before, during and after weaning. Health and production (growth rate and concentrate intakes) were not affected by treatment during the weaning period or over the whole study. Vocalisations were highest post-weaning, and were significantly higher in I calves than pair-reared calves. Furthermore, P28 calves vocalised significantly more than P5 calves. The social network of calves was measured for one month after all calves were grouped in a barn, using association data from spatial proximity loggers. We tested for week-week stability, social differentiation and assortment in the calf network. Additionally, we tested for treatment differences in: coefficient of variation (CV) in association strength, percentage of time spent with ex-penmate (P5 and P28 calves only) and weighted degree centrality (the sum of the strength of an individual’s associations). The network was relatively stable from weeks one to four and was significantly differentiated, with individuals assorting based on prior familiarity. P5 calves had significantly higher CV in association strength than I calves in week one (indicating more heterogeneous social associations) but there were no significant treatment differences in week four. The mean percentage of time that individuals spent with their ex-penmate after regrouping decreased from weeks 1–4, though treatment did not affect this. There were also no significant differences in weighted degree centrality between calves in each rearing treatment. These results suggest that early pair-rearing can allow calves the stress buffering benefits of social support (and that this is more effective when calves are paired earlier) without compromising health or production, and sheds light on the early development of social behaviour in cattle. PMID:28052122

A portable measuring system for a competitive binding glucose biosensor

NASA Astrophysics Data System (ADS)

Colvin, Lydia E.; Means, A. Kristen; Grunlan, Melissa A.; Coté, Gerard L.

2018-02-01

Central to minimizing the long- and short-term complications associated with diabetes is careful monitoring and maintenance of blood glucose at normal levels. Towards replacing conventionally used finger-prick glucose testing, indwelling continuous glucose monitors (CGMs) based on amperometric electrodes have been introduced to the market. Envisioned to lead to a CGM with an increased lifetime, we report herein a fluorescently-labeled competitive binding assay contained within a hydrogel membrane whose glucose response is measured via a novel portable system. The optical system design included a laser source, bifurcated fiber, laser filter and simple fiber coupled spectrometer to obtain the change in FRET pair ratio of the assay. Glucose response of the assay in free solution was measured using this system across the physiologic range (0-200 mg/dL). The FRET pair ratio signal was seen to increase with glucose and the standard error of calibration was 22.42 mg/dL with a MARD value of 14.85%. When the assay was contained within the hydrogel membrane's central cavity and similarly analyzed, the standard error increased but the assay maintained its reversibility.

PlenoPatch: Patch-Based Plenoptic Image Manipulation.

PubMed

Zhang, Fang-Lue; Wang, Jue; Shechtman, Eli; Zhou, Zi-Ye; Shi, Jia-Xin; Hu, Shi-Min

2017-05-01

Patch-based image synthesis methods have been successfully applied for various editing tasks on still images, videos and stereo pairs. In this work we extend patch-based synthesis to plenoptic images captured by consumer-level lenselet-based devices for interactive, efficient light field editing. In our method the light field is represented as a set of images captured from different viewpoints. We decompose the central view into different depth layers, and present it to the user for specifying the editing goals. Given an editing task, our method performs patch-based image synthesis on all affected layers of the central view, and then propagates the edits to all other views. Interaction is done through a conventional 2D image editing user interface that is familiar to novice users. Our method correctly handles object boundary occlusion with semi-transparency, thus can generate more realistic results than previous methods. We demonstrate compelling results on a wide range of applications such as hole-filling, object reshuffling and resizing, changing object depth, light field upscaling and parallax magnification.

Optical power splitter and polarization splitter

NASA Technical Reports Server (NTRS)

Bogert, Gail A. (Inventor)

1988-01-01

A 3.times.3 optical guiding arrangement is disclosed for providing both power splitting between a pair of output guides in the 3.times.3 guide structure and polarization splitting (into the TE and TM modes) between the central guide and the pair of outer guides. In accordance with the present invention, the mutual coupling length L and separation distance d between adjacent guides are chosen to provide the desired polarization splitting and total intensity (power) in the outer guides. For example, an input signal of intensity I comprising both the TE and TM modes may be launched in the center guide and with correct choices for L and d, will result in output signals of I.sub.TM /2 each of the outer pair of guides and I.sub.TE from the central guide.

Modification of the ρ meson detected by low-mass electron-positron pairs in central Pbsbnd Au collisions at 158A GeV/c

NASA Astrophysics Data System (ADS)

Adamová, D.; Agakichiev, G.; Antończyk, D.; Appelshäuser, H.; Belaga, V.; Bielcikova, J.; Braun-Munzinger, P.; Busch, O.; Cherlin, A.; Damjanović, S.; Dietel, T.; Dietrich, L.; Drees, A.; Dubitzky, W.; Esumi, S. I.; Filimonov, K.; Fomenko, K.; Fraenkel, Z.; Garabatos, C.; Glässel, P.; Holeczek, J.; Kushpil, V.; Maas, A.; Marín, A.; Milošević, J.; Milov, A.; Miśkowiec, D.; Panebrattsev, Yu.; Petchenova, O.; Petráček, V.; Pfeiffer, A.; Rak, J.; Ravinovich, I.; Rehak, P.; Sako, H.; Schmitz, W.; Sedykh, S.; Shimansky, S.; Stachel, J.; Šumbera, M.; Tilsner, H.; Tserruya, I.; Wessels, J. P.; Wienold, T.; Wurm, J. P.; Xie, W.; Yurevich, S.; Yurevich, V.; Ceres Collaboration

2008-09-01

We present a measurement of e+e- pair production in central Pbsbnd Au collisions at 158 A GeV / c. As reported earlier, a significant excess of the e+e- pair yield over the expectation from hadron decays is observed. The improved mass resolution of the present data set, recorded with the upgraded CERES experiment at the CERN-SPS, allows for a comparison of the data with different theoretical approaches. The data clearly favor a substantial in-medium broadening of the ρ spectral function over a density-dependent shift of the ρ pole mass. The in-medium broadening model implies that baryon induced interactions are the key mechanism to the observed modifications of the ρ meson at SPS energy.

Modification of the ρ meson detected by low-mass electron positron pairs in central PbAu collisions at 158A GeV/c

NASA Astrophysics Data System (ADS)

Ceres Collaboration; Adamová, D.; Agakichiev, G.; Antończyk, D.; Appelshäuser, H.; Belaga, V.; Bielcikova, J.; Braun-Munzinger, P.; Busch, O.; Cherlin, A.; Damjanović, S.; Dietel, T.; Dietrich, L.; Drees, A.; Dubitzky, W.; Esumi, S. I.; Filimonov, K.; Fomenko, K.; Fraenkel, Z.; Garabatos, C.; Glässel, P.; Holeczek, J.; Kushpil, V.; Maas, A.; Marín, A.; Milošević, J.; Milov, A.; Miśkowiec, D.; Panebrattsev, Yu.; Petchenova, O.; Petráček, V.; Pfeiffer, A.; Rak, J.; Ravinovich, I.; Rehak, P.; Sako, H.; Schmitz, W.; Sedykh, S.; Shimansky, S.; Stachel, J.; Šumbera, M.; Tilsner, H.; Tserruya, I.; Wessels, J. P.; Wienold, T.; Wurm, J. P.; Xie, W.; Yurevich, S.; Yurevich, V.

2008-09-01

We present a measurement of ee pair production in central PbAu collisions at 158A GeV/c. As reported earlier, a significant excess of the ee pair yield over the expectation from hadron decays is observed. The improved mass resolution of the present data set, recorded with the upgraded CERES experiment at the CERN-SPS, allows for a comparison of the data with different theoretical approaches. The data clearly favor a substantial in-medium broadening of the ρ spectral function over a density-dependent shift of the ρ pole mass. The in-medium broadening model implies that baryon induced interactions are the key mechanism to the observed modifications of the ρ meson at SPS energy.

Capturing the radical ion-pair intermediate in DNA guanine oxidation

PubMed Central

Jie, Jialong; Liu, Kunhui; Wu, Lidan; Zhao, Hongmei; Song, Di; Su, Hongmei

2017-01-01

Although the radical ion pair has been frequently invoked as a key intermediate in DNA oxidative damage reactions and photoinduced electron transfer processes, the unambiguous detection and characterization of this species remain formidable and unresolved due to its extremely unstable nature and low concentration. We use the strategy that, at cryogenic temperatures, the transient species could be sufficiently stabilized to be detectable spectroscopically. By coupling the two techniques (the cryogenic stabilization and the time-resolved laser flash photolysis spectroscopy) together, we are able to capture the ion-pair transient G+•⋯Cl− in the chlorine radical–initiated DNA guanine (G) oxidation reaction, and provide direct evidence to ascertain the intricate type of addition/charge separation mechanism underlying guanine oxidation. The unique spectral signature of the radical ion-pair G+•⋯Cl− is identified, revealing a markedly intense absorption feature peaking at 570 nm that is distinctive from G+• alone. Moreover, the ion-pair spectrum is found to be highly sensitive to the protonation equilibria within guanine-cytosine base pair (G:C), which splits into two resolved bands at 480 and 610 nm as the acidic proton transfers along the central hydrogen bond from G+• to C. We thus use this exquisite sensitivity to track the intrabase-pair proton transfer dynamics in the double-stranded DNA oligonucleotides, which is of critical importance for the description of the proton-coupled charge transfer mechanisms in DNA. PMID:28630924

Heterochromatin characterization and ribosomal gene location in two monotypic genera of bloodsucker bugs (Cimicidae, Heteroptera) with holokinetic chromosomes and achiasmatic male meiosis.

PubMed

Poggio, M G; Di Iorio, O; Turienzo, P; Papeschi, A G; Bressa, M J

2014-12-01

Members of the family Cimicidae (Heteroptera: Cimicomorpha) are temporary bloodsuckers on birds and bats as primary hosts and humans as secondary hosts. Acanthocrios furnarii (2n=12=10+XY, male) and Psitticimex uritui (2n=31=28+X1X2Y, male) are two monotypic genera of the subfamily Haematosiphoninae, which have achiasmatic male meiosis of collochore type. Here, we examined chromatin organization and constitution of cimicid holokinetic chromosomes by determining the amount, composition and distribution of constitutive heterochromatin, and number and location of nucleolus organizer regions (NORs) in both species. Results showed that these two bloodsucker bugs possess high heterochromatin content and have an achiasmatic male meiosis, in which three regions can be differentiated in each autosomal bivalent: (i) terminal heterochromatic regions in repulsion; (ii) a central region, where the homologous chromosomes are located parallel but without contact between them; and (iii) small areas within the central region, where collochores are detected. Acanthocrios furnarii presented a single NOR on an autosomal pair, whereas P. uritui presented two NORs, one on an autosomal pair and the other on a sex chromosome. All NORs were found to be associated with CMA3 bright bands, indicating that the whole rDNA repeating unit is rich in G+C base pairs. Based on the variations in the diploid autosomal number, the presence of simple and multiple sex chromosome systems, and the number and location of 18S rDNA loci in the two Cimicidae species studied, we might infer that rDNA clusters and genome are highly dynamic among the representatives of this family.

A small modified hammerhead ribozyme and its conformational characteristics determined by mutagenesis and lattice calculation.

PubMed Central

Lustig, B; Lin, N H; Smith, S M; Jernigan, R L; Jeang, K T

1995-01-01

A prototypic hammerhead ribozyme has three helices that surround an asymmetrical central core loop. We have mutagenized a hammerhead type ribozyme. In agreement with previous studies, progressive removal of stem-loop II from a three stemmed ribozyme showed that this region is not absolutely critical for catalysis. However, complete elimination of stem II and its loop did reduce, but did not eliminate, function. In a stem-loop II-deleted ribozyme, activity was best preserved when a purine, preferably a G, was present at position 10.1. This G contributed to catalysis irregardless of its role as either one part of a canonical pair with a C residue at 11.1 or a lone nucleotide with C (11.1) deleted. Computational methods using lattices generated 87 million three-dimensional chain forms for a stem-loop II-deleted RNA complex that preserved one potential G.C base pair at positions 10.1 and 11.1. This exhaustive set of chain forms included one major class of structures with G(10.1) being spatially proximal to the GUCX cleavage site of the substrate strand. Strong correlations were observed between colinear arrangement of stems I and III, constraints of base-pairing in the central core loop, and one particular placement of G(10.1) relative to the cleavage site. Our calculations of a stem-loop II-deleted ribozyme indicate that without needing to invoke any other constraints, the inherent asymmetry in the lengths of the two loop strands (3 nt in one and 7 nt in the other) that compose the core and flank G10.1-C11.1 stipulated strongly this particular G placement. This suggests that the hammerhead ribozyme maintains an asymmetry in its internal loop for a necessary structure/function reason. Images PMID:7567466

Central oxytocin receptors mediate mating-induced partner preferences and enhance correlated activation across forebrain nuclei in male prairie voles.

PubMed

Johnson, Zachary V; Walum, Hasse; Jamal, Yaseen A; Xiao, Yao; Keebaugh, Alaine C; Inoue, Kiyoshi; Young, Larry J

2016-03-01

Oxytocin (OT) is a deeply conserved nonapeptide that acts both peripherally and centrally to modulate reproductive physiology and sociosexual behavior across divergent taxa, including humans. In vertebrates, the distribution of the oxytocin receptor (OTR) in the brain is variable within and across species, and OTR signaling is critical for a variety of species-typical social and reproductive behaviors, including affiliative and pair bonding behaviors in multiple socially monogamous lineages of fishes, birds, and mammals. Early work in prairie voles suggested that the endogenous OT system modulates mating-induced partner preference formation in females but not males; however, there is significant evidence that central OTRs may modulate pair bonding behavior in both sexes. In addition, it remains unclear how transient windows of central OTR signaling during sociosexual interaction modulate neural activity to produce enduring shifts in sociobehavioral phenotypes, including the formation of selective social bonds. Here we re-examine the role of the central OT system in partner preference formation in male prairie voles using a selective OTR antagonist delivered intracranially. We then use the same antagonist to examine how central OTRs modulate behavior and immediate early gene (Fos) expression, a metric of neuronal activation, in males during brief sociosexual interaction with a female. Our results suggest that, as in females, OTR signaling is critical for partner preference formation in males and enhances correlated activation across sensory and reward processing brain areas during sociosexual interaction. These results are consistent with the hypothesis that central OTR signaling facilitates social bond formation by coordinating activity across a pair bonding neural network. Copyright © 2015 Elsevier Inc. All rights reserved.

Balancing act: Evidence for a strong subdominant d -wave pairing channel in Ba 0.6 K 0.4 Fe 2 As 2

DOE PAGES

Böhm, T.; Kemper, A. F.; Moritz, B.; ...

2014-12-18

We present detailed measurements of the temperature-dependent Raman spectra of optimally doped Ba 0.6K 0.4Fe 2As 2 and analyze the low-temperature spectra based on local-density-approximation band-structure calculations and the subsequent estimation of effective Raman vertices. Experimentally, a narrow, emergent mode appears in the B 1g (d x2-y2) Raman spectra only below T c, well into the superconducting state and at an energy below twice the energy gap on the electron Fermi-surface sheets. The Raman spectra can be reproduced quantitatively with estimates for the magnitude and momentum-space structure of an A 1g (s-wave) pairing gap on different Fermi-surface sheets, as wellmore » as the identification of the emergent sharp feature as a Bardasis-Schrieffer exciton. Formed as a Cooper-pair bound state in a subdominant d x2-y2 channel, the binding energy of the exciton relative to the gap edge shows that the coupling strength in the subdominant channel is as strong as 60% of that in the dominant s-wave channel. This result suggests that d x2-y2 may be the dominant pairing symmetry in Fe-based superconductors that lack central hole bands.« less

Gloves Reprocessing: Does It Really Save Money?

PubMed

Arora, Pankaj; Kumari, Santosh; Sodhi, Jitender; Talati, Shweta; Gupta, Anil Kumar

2015-12-01

Gloves are reprocessed and reused in health-care facilities in resource-limited settings to reduce the cost of availability of gloves. The study was done with the aim to compute the cost of reprocessing of gloves so that an economically rationale decision can be taken. A retrospective record-based cross-sectional study was undertaken in a central sterile supply department where different steps during reprocessing of gloves were identified and the cost involved in reprocessing per pair of gloves was calculated. The cost of material and manpower was calculated to arrive at the cost of reprocessing per pair of gloves. The cost of a reprocessed pair of surgical gloves was calculated to be Indian Rupee (INR) 14.33 which was greater than the cost of a new pair of disposable surgical gloves (INR 9.90) as the cost of sterilization of one pair of gloves itself came out to  be INR 10.97. The current study showed that the purchase of sterile disposable single-use gloves is cheaper than the process of recycling. Reprocessing of gloves is not economical on tangible terms even in resource-limited settings, and from the perspective of better infection control as well as health-care worker safety, it further justifies the use of disposable gloves.

Fluctuation scaling of quotation activities in the foreign exchange market

NASA Astrophysics Data System (ADS)

Sato, Aki-Hiro; Nishimura, Maiko; Hołyst, Janusz A.

2010-07-01

We study the scaling behavior of quotation activities for various currency pairs in the foreign exchange market. The components’ centrality is estimated from multiple time series and visualized as a currency pair network. The power-law relationship between a mean of quotation activity and its standard deviation for each currency pair is found. The scaling exponent α and the ratio between common and specific fluctuations η increase with the length of the observation time window Δt. The result means that although for Δt=1 (min), the market dynamics are governed by specific processes, and at a longer time scale Δt>100 (min) the common information flow becomes more important. We point out that quotation activities are not independently Poissonian for Δt=1 (min), and temporally or mutually correlated activities of quotations can happen even at this time scale. A stochastic model for the foreign exchange market based on a bipartite graph representation is proposed.

Esthetic evaluation of dental and gingival asymmetries.

PubMed

Fernandes, Liliana; Pinho, Teresa

2015-06-01

The aim of this study was to determine which smile asymmetries were less esthetic, dental or gingival. Laypeople (297), generalists (223), prosthodontists (50) and orthodontists (49), evaluated the esthetics of digitally-modified images taken from the same frontal intra-oral photograph, using the same lips, simulating upper maxillary midline shift, occlusal plane inclination, asymmetric incisal edge and asymmetric gingival migration. The images were later paired into 3 groups. The only ones considered esthetic were the asymmetric incisal edge of the 0.5 mm shorter upper central incisor and the asymmetric gingival migration (2 mm) of the upper central incisor. In the paired images, upper maxillary midline shift vs. occlusal plane inclination, the former was rated less esthetic, while in the asymmetric incisal edge vs. asymmetric gingival migration pair, the latter was considered to be less esthetic. Laypeople and generalists consider smiles more attractive. The only images considered esthetic were the asymmetric incisal edge of the central incisor shorter by 0.5 mm and the 2 mm asymmetric gingival migration of the upper central incisor. In the horizontal plane (maxillary midline shift vs. occlusal plane cant), the dental asymmetries were considered less esthetic than the gingival asymmetries. However, in the vertical plane (asymmetric incisal edge vs. asymmetric gingival migration) the opposite was recorded. Copyright © 2015 CEO. Published by Elsevier Masson SAS. All rights reserved.

Bonding in Heavier Group 14 Zero-Valent Complexes-A Combined Maximum Probability Domain and Valence Bond Theory Approach.

PubMed

Turek, Jan; Braïda, Benoît; De Proft, Frank

2017-10-17

The bonding in heavier Group 14 zero-valent complexes of a general formula L 2 E (E=Si-Pb; L=phosphine, N-heterocyclic and acyclic carbene, cyclic tetrylene and carbon monoxide) is probed by combining valence bond (VB) theory and maximum probability domain (MPD) approaches. All studied complexes are initially evaluated on the basis of the structural parameters and the shape of frontier orbitals revealing a bent structural motif and the presence of two lone pairs at the central E atom. For the VB calculations three resonance structures are suggested, representing the "ylidone", "ylidene" and "bent allene" structures, respectively. The influence of both ligands and central atoms on the bonding situation is clearly expressed in different weights of the resonance structures for the particular complexes. In general, the bonding in the studied E 0 compounds, the tetrylones, is best described as a resonating combination of "ylidone" and "ylidene" structures with a minor contribution of the "bent allene" structure. Moreover, the VB calculations allow for a straightforward assessment of the π-backbonding (E→L) stabilization energy. The validity of the suggested resonance model is further confirmed by the complementary MPD calculations focusing on the E lone pair region as well as the E-L bonding region. Likewise, the MPD method reveals a strong influence of the σ-donating and π-accepting properties of the ligand. In particular, either one single domain or two symmetrical domains are found in the lone pair region of the central atom, supporting the predominance of either the "ylidene" or "ylidone" structures having one or two lone pairs at the central atom, respectively. Furthermore, the calculated average populations in the lone pair MPDs correlate very well with the natural bond orbital (NBO) populations, and can be related to the average number of electrons that is backdonated to the ligands. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The presence of codon-anticodon pairs in the acceptor stem of tRNAs.

PubMed Central

Rodin, S; Rodin, A; Ohno, S

1996-01-01

A total of 1268 available (excluding mitochondrial) tRNA sequences was used to reconstruct the common consensus image of their acceptor domains. Its structure appeared as a 11-bp-long double-stranded palindrome with complementary triplets in the center, each flanked by the 3'-ACCD and NGGU-5' motifs on each strand (D, base determinator). The palindrome readily extends up to the modern tRNA-like cloverleaf passing through an intermediate hairpin having in the center the single-stranded triplet, in supplement to its double-stranded precursor. The latter might represent an original anticodon-codon pair mapped at 1-2-3 positions of the present-day tRNA acceptors. This conclusion is supported by the striking correlation: in pairs of consensus tRNAs with complementary anticodons, their bases at the 2nd position of the acceptor stem were also complementary. Accordingly, inverse complementarity was also evident at the 71st position of the acceptor stem. With a single exception (tRNA(Phe)-tRNA(Glu) pair), the parallelism is especially impressive for the pairs of tRNAs recognized by aminoacyl-tRNA synthetases (aaRS) from the opposite classes. The above complementarity still doubly presented at the key central position of real single-stranded anticodons and their hypothetical double-stranded precursors is consistent with our previous data pointing to the double-strand use of ancient RNAs in the origin of the main actors in translation- tRNAs with complementary anticodons and the two classes of aaRS. Images Fig. 3 Table 2 Fig. 4 PMID:8643439

Microscale ion trap mass spectrometer

DOEpatents

Ramsey, J. Michael; Witten, William B.; Kornienko, Oleg

2002-01-01

An ion trap for mass spectrometric chemical analysis of ions is delineated. The ion trap includes a central electrode having an aperture; a pair of insulators, each having an aperture; a pair of end cap electrodes, each having an aperture; a first electronic signal source coupled to the central electrode; a second electronic signal source coupled to the end cap electrodes. The central electrode, insulators, and end cap electrodes are united in a sandwich construction where their respective apertures are coaxially aligned and symmetric about an axis to form a partially enclosed cavity having an effective radius r.sub.0 and an effective length 2z.sub.0, wherein r.sub.0 and/or z.sub.0 are less than 1.0 mm, and a ratio z.sub.0 /r.sub.0 is greater than 0.83.

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

Bromberger, Seth A.; Klymko, Christine F.; Henderson, Keith A.

Betweenness centrality is a graph statistic used to nd vertices that are participants in a large number of shortest paths in a graph. This centrality measure is commonly used in path and network interdiction problems and its complete form requires the calculation of all-pairs shortest paths for each vertex. This leads to a time complexity of O(jV jjEj), which is impractical for large graphs. Estimation of betweenness centrality has focused on performing shortest-path calculations on a subset of randomly- selected vertices. This reduces the complexity of the centrality estimation to O(jSjjEj); jSj < jV j, which can be scaled appropriatelymore » based on the computing resources available. An estimation strategy that uses random selection of vertices for seed selection is fast and simple to implement, but may not provide optimal estimation of betweenness centrality when the number of samples is constrained. Our experimentation has identi ed a number of alternate seed-selection strategies that provide lower error than random selection in common scale-free graphs. These strategies are discussed and experimental results are presented.« less

Easy Words: Reference Resolution in a Malevolent Referent World.

PubMed

Gleitman, Lila R; Trueswell, John C

2018-06-15

This article describes early stages in the acquisition of a first vocabulary by infants and young children. It distinguishes two major stages, the first of which operates by a stand-alone word-to-world pairing procedure and the second of which, using the evidence so acquired, builds a domain-specific syntax-sensitive structure-to-world pairing procedure. As we show, the first stage of learning is slow, restricted in character, and to some extent errorful, whereas the second procedure is determinative, rapid, and essentially errorless. Our central claim here is that the early, referentially based learning procedure succeeds at all because it is reined in by attention-focusing properties of word-to-world timing and related indicants of referential intent. Copyright © 2018 Cognitive Science Society, Inc.

Sordaria, a model system to uncover links between meiotic pairing and recombination

PubMed Central

Zickler, Denise; Espagne, Eric

2017-01-01

The mycelial fungus Sordaria macrospora was first used as experimental system for meiotic recombination. This review shows that it provides also a powerful cytological system for dissecting chromosome dynamics in wild-type and mutant meioses. Fundamental cytogenetic findings include: (1) The identification of presynaptic alignment as a key step in pairing of homologous chromosomes. (2) The discovery that biochemical complexes that mediate recombination at the DNA level concomitantly mediate pairing of homologs. (3) This pairing process involves not only resolution but also avoidance of chromosomal entanglements and the resolution system includes dissolution of constraining DNA recombination interactions, achieved by a unique role of Mlh1. (4) Discovery that the central components of the synaptonemal complex directly mediate the re-localization of the recombination proteins from on-axis to in-between homologue axis positions. (5) Identification of putative STUbL protein Hei10 as a structure-based signal transduction molecule that coordinates progression and differentiation of recombinational interactions at multiple stages. (6) Discovery that a single interference process mediates both nucleation of the SC and designation of crossover sites, thereby ensuring even spacing of both features. (7) Discovery of local modulation of sister-chromatid cohesion at sites of crossover recombination. PMID:26877138

Structural basis of DNA bending and oriented heterodimer binding by the basic leucine zipper domains of Fos and Jun.

PubMed

Leonard, D A; Rajaram, N; Kerppola, T K

1997-05-13

Interactions among transcription factors that bind to separate sequence elements require bending of the intervening DNA and juxtaposition of interacting molecular surfaces in an appropriate orientation. Here, we examine the effects of single amino acid substitutions adjacent to the basic regions of Fos and Jun as well as changes in sequences flanking the AP-1 site on DNA bending. Substitution of charged amino acid residues at positions adjacent to the basic DNA-binding domains of Fos and Jun altered DNA bending. The change in DNA bending was directly proportional to the change in net charge for all heterodimeric combinations between these proteins. Fos and Jun induced distinct DNA bends at different binding sites. Exchange of a single base pair outside of the region contacted in the x-ray crystal structure altered DNA bending. Substitution of base pairs flanking the AP-1 site had converse effects on the opposite directions of DNA bending induced by homodimers and heterodimers. These results suggest that Fos and Jun induce DNA bending in part through electrostatic interactions between amino acid residues adjacent to the basic region and base pairs flanking the AP-1 site. DNA bending by Fos and Jun at inverted binding sites indicated that heterodimers bind to the AP-1 site in a preferred orientation. Mutation of a conserved arginine within the basic regions of Fos and transversion of the central C:G base pair in the AP-1 site to G:C had complementary effects on the orientation of heterodimer binding and DNA bending. The conformational variability of the Fos-Jun-AP-1 complex may contribute to its functional versatility at different promoters.

Records of Migration in the Exoplanet Configurations

NASA Astrophysics Data System (ADS)

Michtchenko, Tatiana A.; Rodriguez Colucci, A.; Tadeu Dos Santos, M.

2013-05-01

Abstract (2,250 Maximum Characters): When compared to our Solar System, many exoplanet systems exhibit quite unusual planet configurations; some of these are hot Jupiters, which orbit their central stars with periods of a few days, others are resonant systems composed of two or more planets with commensurable orbital periods. It has been suggested that these configurations can be the result of a migration processes originated by tidal interactions of the planets with disks and central stars. The process known as planet migration occurs due to dissipative forces which affect the planetary semi-major axes and cause the planets to move towards to, or away from, the central star. In this talk, we present possible signatures of planet migration in the distribution of the hot Jupiters and resonant exoplanet pairs. For this task, we develop a semi-analytical model to describe the evolution of the migrating planetary pair, based on the fundamental concepts of conservative and dissipative dynamics of the three-body problem. Our approach is based on an analysis of the energy and the orbital angular momentum exchange between the two-planet system and an external medium; thus no specific kind of dissipative forces needs to be invoked. We show that, under assumption that dissipation is weak and slow, the evolutionary routes of the migrating planets are traced by the stationary solutions of the conservative problem (Birkhoff, Dynamical systems, 1966). The ultimate convergence and the evolution of the system along one of these modes of motion are determined uniquely by the condition that the dissipation rate is sufficiently smaller than the roper frequencies of the system. We show that it is possible to reassemble the starting configurations and migration history of the systems on the basis of their final states, and consequently to constrain the parameters of the physical processes involved.

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

DOE PAGES

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

2016-10-19

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

Compliance Testing of Eielson Air Force Base Central Heating and Power Plant, Coal Fired Boiler Number 3, Eielson Air Force Base, Alaska

DTIC Science & Technology

1988-12-01

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Anisotropy in pair dispersion of inertial particles in turbulent channel flow

NASA Astrophysics Data System (ADS)

Pitton, Enrico; Marchioli, Cristian; Lavezzo, Valentina; Soldati, Alfredo; Toschi, Federico

2012-07-01

The rate at which two particles separate in turbulent flows is of central importance to predict the inhomogeneities of particle spatial distribution and to characterize mixing. Pair separation is analyzed for the specific case of small, inertial particles in turbulent channel flow to examine the role of mean shear and small-scale turbulent velocity fluctuations. To this aim an Eulerian-Lagrangian approach based on pseudo-spectral direct numerical simulation (DNS) of fully developed gas-solid flow at shear Reynolds number Reτ = 150 is used. Pair separation statistics have been computed for particles with different inertia (and for inertialess tracers) released from different regions of the channel. Results confirm that shear-induced effects predominate when the pair separation distance becomes comparable to the largest scale of the flow. Results also reveal the fundamental role played by particles-turbulence interaction at the small scales in triggering separation during the initial stages of pair dispersion. These findings are discussed examining Lagrangian observables, including the mean square separation, which provide prima facie evidence that pair dispersion in non-homogeneous anisotropic turbulence has a superdiffusive nature and may generate non-Gaussian number density distributions of both particles and tracers. These features appear to persist even when the effects of shear dispersion are filtered out, and exhibit strong dependency on particle inertia. Application of present results is discussed in the context of modelling approaches for particle dispersion in wall-bounded turbulent flows.

Structural and Functional Basis of the Fidelity of Nucleotide Selection by Flavivirus RNA-Dependent RNA Polymerases

PubMed Central

Canard, Bruno

2018-01-01

Viral RNA-dependent RNA polymerases (RdRps) play a central role not only in viral replication, but also in the genetic evolution of viral RNAs. After binding to an RNA template and selecting 5′-triphosphate ribonucleosides, viral RdRps synthesize an RNA copy according to Watson-Crick base-pairing rules. The copy process sometimes deviates from both the base-pairing rules specified by the template and the natural ribose selectivity and, thus, the process is error-prone due to the intrinsic (in)fidelity of viral RdRps. These enzymes share a number of conserved amino-acid sequence strings, called motifs A–G, which can be defined from a structural and functional point-of-view. A co-relation is gradually emerging between mutations in these motifs and viral genome evolution or observed mutation rates. Here, we review our current knowledge on these motifs and their role on the structural and mechanistic basis of the fidelity of nucleotide selection and RNA synthesis by Flavivirus RdRps. PMID:29385764

Discriminating tastes

PubMed Central

Storz, Gisela

2011-01-01

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

A Novel Optimal Joint Resource Allocation Method in Cooperative Multicarrier Networks: Theory and Practice

PubMed Central

Gao, Yuan; Zhou, Weigui; Ao, Hong; Chu, Jian; Zhou, Quan; Zhou, Bo; Wang, Kang; Li, Yi; Xue, Peng

2016-01-01

With the increasing demands for better transmission speed and robust quality of service (QoS), the capacity constrained backhaul gradually becomes a bottleneck in cooperative wireless networks, e.g., in the Internet of Things (IoT) scenario in joint processing mode of LTE-Advanced Pro. This paper focuses on resource allocation within capacity constrained backhaul in uplink cooperative wireless networks, where two base stations (BSs) equipped with single antennae serve multiple single-antennae users via multi-carrier transmission mode. In this work, we propose a novel cooperative transmission scheme based on compress-and-forward with user pairing to solve the joint mixed integer programming problem. To maximize the system capacity under the limited backhaul, we formulate the joint optimization problem of user sorting, subcarrier mapping and backhaul resource sharing among different pairs (subcarriers for users). A novel robust and efficient centralized algorithm based on alternating optimization strategy and perfect mapping is proposed. Simulations show that our novel method can improve the system capacity significantly under the constraint of the backhaul resource compared with the blind alternatives. PMID:27077865

Charged-Particle Multiplicity Density at Midrapidity in Central Pb-Pb Collisions at sNN=2.76TeV

NASA Astrophysics Data System (ADS)

Aamodt, K.; Abelev, B.; Abrahantes Quintana, A.; Adamová, D.; Adare, A. M.; Aggarwal, M. M.; Aglieri Rinella, G.; Agocs, A. G.; Aguilar Salazar, S.; Ahammed, Z.; Ahmad Masoodi, A.; Ahmad, N.; Ahn, S. U.; Akindinov, A.; Aleksandrov, D.; Alessandro, B.; Alfaro Molina, R.; Alici, A.; Alkin, A.; Almaráz Aviña, E.; Alt, T.; Altini, V.; Altinpinar, S.; Altsybeev, I.; Andrei, C.; Andronic, A.; Anguelov, V.; Anson, C.; Antičić, T.; Antinori, F.; Antonioli, P.; Aphecetche, L.; Appelshäuser, H.; Arbor, N.; Arcelli, S.; Arend, A.; Armesto, N.; Arnaldi, R.; Aronsson, T.; Arsene, I. C.; Asryan, A.; Augustinus, A.; Averbeck, R.; Awes, T. C.; Äystö, J.; Azmi, M. D.; Bach, M.; Badalà, A.; Baek, Y. W.; Bagnasco, S.; Bailhache, R.; Bala, R.; Baldini Ferroli, R.; Baldisseri, A.; Baldit, A.; Baltasar Dos Santos Pedrosa, F.; Bán, J.; Barbera, R.; Barile, F.; Barnaföldi, G. G.; Barnby, L. S.; Barret, V.; Bartke, J.; Basile, M.; Bastid, N.; Bathen, B.; Batigne, G.; Batyunya, B.; Baumann, C.; Bearden, I. G.; Beck, H.; Belikov, I.; Bellini, F.; Bellwied, R.; Belmont-Moreno, E.; Beole, S.; Berceanu, I.; Bercuci, A.; Berdermann, E.; Berdnikov, Y.; Bergmann, C.; Betev, L.; Bhasin, A.; Bhati, A. K.; Bianchi, L.; Bianchi, N.; Bianchin, C.; Bielčík, J.; Bielčíková, J.; Bilandzic, A.; Biolcati, E.; Blanc, A.; Blanco, F.; Blanco, F.; Blau, D.; Blume, C.; Boccioli, M.; Bock, N.; Bogdanov, A.; Bøggild, H.; Bogolyubsky, M.; Boldizsár, L.; Bombara, M.; Bombonati, C.; Book, J.; Borel, H.; Borissov, A.; Bortolin, C.; Bose, S.; Bossú, F.; Botje, M.; Böttger, S.; Boyer, B.; Braun-Munzinger, P.; Bravina, L.; Bregant, M.; Breitner, T.; Broz, M.; Brun, R.; Bruna, E.; Bruno, G. E.; Budnikov, D.; Buesching, H.; Bugaiev, K.; Busch, O.; Buthelezi, Z.; Caffarri, D.; Cai, X.; Caines, H.; Calvo Villar, E.; Camerini, P.; Canoa Roman, V.; Cara Romeo, G.; Carena, F.; Carena, W.; Carminati, F.; Casanova Díaz, A.; Caselle, M.; Castillo Castellanos, J.; Catanescu, V.; Cavicchioli, C.; Cepila, J.; Cerello, P.; Chang, B.; Chapeland, S.; Charvet, J. L.; Chattopadhyay, S.; Chattopadhyay, S.; Cherney, M.; Cheshkov, C.; Cheynis, B.; Chiavassa, E.; Chibante Barroso, V.; Chinellato, D. D.; Chochula, P.; Chojnacki, M.; Christakoglou, P.; Christensen, C. H.; Christiansen, P.; Chujo, T.; Cicalo, C.; Cifarelli, L.; Cindolo, F.; Cleymans, J.; Coccetti, F.; Coffin, J.-P.; Coli, S.; Conesa Balbastre, G.; Conesa Del Valle, Z.; Constantin, P.; Contin, G.; Contreras, J. G.; Cormier, T. M.; Corrales Morales, Y.; Cortés Maldonado, I.; Cortese, P.; Cosentino, M. R.; Costa, F.; Cotallo, M. E.; Crescio, E.; Crochet, P.; Cuautle, E.; Cunqueiro, L.; Erasmo, G. D.; Dainese, A.; Dalsgaard, H. H.; Danu, A.; Das, D.; Das, I.; Das, K.; Dash, A.; Dash, S.; de, S.; de Azevedo Moregula, A.; de Barros, G. O. V.; de Caro, A.; de Cataldo, G.; de Cuveland, J.; de Falco, A.; de Gruttola, D.; de Marco, N.; de Pasquale, S.; de Remigis, R.; de Rooij, R.; Debski, P. R.; Del Castillo Sanchez, E.; Delagrange, H.; Delgado Mercado, Y.; Dellacasa, G.; Deloff, A.; Demanov, V.; Dénes, E.; Deppman, A.; di Bari, D.; di Giglio, C.; di Liberto, S.; di Mauro, A.; di Nezza, P.; Dietel, T.; Divià, R.; Djuvsland, Ø.; Dobrin, A.; Dobrowolski, T.; Domínguez, I.; Dönigus, B.; Dordic, O.; Driga, O.; Dubey, A. K.; Dubuisson, J.; Ducroux, L.; Dupieux, P.; Dutta Majumdar, A. K.; Dutta Majumdar, M. R.; Elia, D.; Emschermann, D.; Engel, H.; Erdal, H. A.; Espagnon, B.; Estienne, M.; Esumi, S.; Evans, D.; Evrard, S.; Eyyubova, G.; Fabjan, C. W.; Fabris, D.; Faivre, J.; Falchieri, D.; Fantoni, A.; Fasel, M.; Fearick, R.; Fedunov, A.; Fehlker, D.; Fekete, V.; Felea, D.; Feofilov, G.; Fernández Téllez, A.; Ferretti, A.; Ferretti, R.; Figiel, J.; Figueredo, M. A. S.; Filchagin, S.; Fini, R.; Finogeev, D.; Fionda, F. M.; Fiore, E. M.; Floris, M.; Foertsch, S.; Foka, P.; Fokin, S.; Fragiacomo, E.; Fragkiadakis, M.; Frankenfeld, U.; Fuchs, U.; Furano, F.; Furget, C.; Fusco Girard, M.; Gaardhøje, J. J.; Gadrat, S.; Gagliardi, M.; Gago, A.; Gallio, M.; Gangadharan, D. R.; Ganoti, P.; Ganti, M. S.; Garabatos, C.; Garcia-Solis, E.; Garishvili, I.; Gemme, R.; Gerhard, J.; Germain, M.; Geuna, C.; Gheata, A.; Gheata, M.; Ghidini, B.; Ghosh, P.; Gianotti, P.; Girard, M. R.; Giraudo, G.; Giubellino, P.; Gladysz-Dziadus, E.; Glässel, P.; Gomez, R.; Ferreiro, E. G.; González Santos, H.; González-Trueba, L. H.; González-Zamora, P.; Gorbunov, S.; Gotovac, S.; Grabski, V.; Grajcarek, R.; Grelli, A.; Grigoras, A.; Grigoras, C.; Grigoriev, V.; Grigoryan, A.; Grigoryan, S.; Grinyov, B.; Grion, N.; Gros, P.; Grosse-Oetringhaus, J. F.; Grossiord, J.-Y.; Grosso, R.; Guber, F.; Guernane, R.; Guerra Gutierrez, C.; Guerzoni, B.; Gulbrandsen, K.; Gunji, T.; Gupta, A.; Gupta, R.; Gutbrod, H.; Haaland, Ø.; Hadjidakis, C.; Haiduc, M.; Hamagaki, H.; Hamar, G.; Harris, J. W.; Hartig, M.; Hasch, D.; Hasegan, D.; Hatzifotiadou, D.; Hayrapetyan, A.; Heide, M.; Heinz, M.; Helstrup, H.; Herghelegiu, A.; Hernández, C.; Herrera Corral, G.; Herrmann, N.; Hetland, K. F.; Hicks, B.; Hille, P. T.; Hippolyte, B.; Horaguchi, T.; Hori, Y.; Hristov, P.; Hřivnáčová, I.; Huang, M.; Huber, S.; Humanic, T. J.; Hwang, D. S.; Ichou, R.; Ilkaev, R.; Ilkiv, I.; Inaba, M.; Incani, E.; Innocenti, G. M.; Innocenti, P. G.; Ippolitov, M.; Irfan, M.; Ivan, C.; Ivanov, A.; Ivanov, M.; Ivanov, V.; Jachołkowski, A.; Jacobs, P. M.; Jancurová, L.; Jangal, S.; Janik, R.; Jena, S.; Jirden, L.; Jones, G. T.; Jones, P. G.; Jovanović, P.; Jung, H.; Jung, W.; Jusko, A.; Kalcher, S.; Kaliňák, P.; Kalisky, M.; Kalliokoski, T.; Kalweit, A.; Kamermans, R.; Kanaki, K.; Kang, E.; Kang, J. H.; Kaplin, V.; Karavichev, O.; Karavicheva, T.; Karpechev, E.; Kazantsev, A.; Kebschull, U.; Keidel, R.; Khan, M. M.; Khan, S. A.; Khanzadeev, A.; Kharlov, Y.; Kileng, B.; Kim, D. J.; Kim, D. S.; Kim, D. W.; Kim, H. N.; Kim, J. H.; Kim, J. S.; Kim, M.; Kim, M.; Kim, S.; Kim, S. H.; Kirsch, S.; Kisel, I.; Kiselev, S.; Kisiel, A.; Klay, J. L.; Klein, J.; Klein-Bösing, C.; Kliemant, M.; Klovning, A.; Kluge, A.; Knichel, M. L.; Koch, K.; Köhler, M. K.; Kolevatov, R.; Kolojvari, A.; Kondratiev, V.; Kondratyeva, N.; Konevskih, A.; Kornaś, E.; Kottachchi Kankanamge Don, C.; Kour, R.; Kowalski, M.; Kox, S.; Koyithatta Meethaleveedu, G.; Kozlov, K.; Kral, J.; Králik, I.; Kramer, F.; Kraus, I.; Krawutschke, T.; Kretz, M.; Krivda, M.; Krizek, F.; Krumbhorn, D.; Krus, M.; Kryshen, E.; Krzewicki, M.; Kucheriaev, Y.; Kuhn, C.; Kuijer, P. G.; Kurashvili, P.; Kurepin, A.; Kurepin, A. B.; Kuryakin, A.; Kushpil, S.; Kushpil, V.; Kweon, M. J.; Kwon, Y.; La Rocca, P.; Ladrón de Guevara, P.; Lafage, V.; Lara, C.; Lardeux, A.; Larsen, D. T.; Lazzeroni, C.; Le Bornec, Y.; Lea, R.; Lee, K. S.; Lee, S. C.; Lefèvre, F.; Lehnert, J.; Leistam, L.; Lenhardt, M.; Lenti, V.; León Monzón, I.; León Vargas, H.; Lévai, P.; Li, X.; Lien, J.; Lietava, R.; Lindal, S.; Lindenstruth, V.; Lippmann, C.; Lisa, M. A.; Liu, L.; Loenne, P. I.; Loggins, V. R.; Loginov, V.; Lohn, S.; Loizides, C.; Loo, K. K.; Lopez, X.; López Noriega, M.; López Torres, E.; Løvhøiden, G.; Lu, X.-G.; Luettig, P.; Lunardon, M.; Luparello, G.; Luquin, L.; Luzzi, C.; Ma, K.; Ma, R.; Madagodahettige-Don, D. M.; Maevskaya, A.; Mager, M.; Mahapatra, D. P.; Maire, A.; Mal'Kevich, D.; Malaev, M.; Maldonado Cervantes, I.; Malinina, L.; Malzacher, P.; Mamonov, A.; Manceau, L.; Mangotra, L.; Manko, V.; Manso, F.; Manzari, V.; Mao, Y.; Mareš, J.; Margagliotti, G. V.; Margotti, A.; Marín, A.; Markert, C.; Martashvili, I.; Martinengo, P.; Martínez, M. I.; Martínez Davalos, A.; Martínez García, G.; Martynov, Y.; Masciocchi, S.; Masera, M.; Masoni, A.; Massacrier, L.; Mastromarco, M.; Mastroserio, A.; Matthews, Z. L.; Matyja, A.; Mayani, D.; Mayer, C.; Mazza, G.; Mazzoni, M. A.; Meddi, F.; Menchaca-Rocha, A.; Mendez Lorenzo, P.; Menis, I.; Mercado Pérez, J.; Meres, M.; Mereu, P.; Miake, Y.; Midori, J.; Milano, L.; Milosevic, J.; Mischke, A.; Miśkowiec, D.; Mitu, C.; Mlynarz, J.; Mohanty, A. K.; Mohanty, B.; Molnar, L.; Montaño Zetina, L.; Monteno, M.; Montes, E.; Morando, M.; Moreira de Godoy, D. A.; Moretto, S.; Morsch, A.; Muccifora, V.; Mudnic, E.; Muhuri, S.; Müller, H.; Munhoz, M. G.; Munoz, J.; Musa, L.; Musso, A.; Nandi, B. K.; Nania, R.; Nappi, E.; Nattrass, C.; Navach, F.; Navin, S.; Nayak, T. K.; Nazarenko, S.; Nazarov, G.; Nedosekin, A.; Nendaz, F.; Newby, J.; Nicassio, M.; Nielsen, B. S.; Niida, T.; Nikolaev, S.; Nikolic, V.; Nikulin, S.; Nikulin, V.; Nilsen, B. S.; Nilsson, M. S.; Noferini, F.; Nooren, G.; Novitzky, N.; Nyanin, A.; Nyatha, A.; Nygaard, C.; Nystrand, J.; Obayashi, H.; Ochirov, A.; Oeschler, H.; Oh, S. K.; Oleniacz, J.; Oppedisano, C.; Ortiz Velasquez, A.; Ortona, G.; Oskarsson, A.; Ostrowski, P.; Otterlund, I.; Otwinowski, J.; Oyama, K.; Ozawa, K.; Pachmayer, Y.; Pachr, M.; Padilla, F.; Pagano, P.; Jayarathna, S. P.; Paić, G.; Painke, F.; Pajares, C.; Pal, S.; Pal, S. K.; Palaha, A.; Palmeri, A.; Pappalardo, G. S.; Park, W. J.; Patalakha, D. I.; Paticchio, V.; Pavlinov, A.; Pawlak, T.; Peitzmann, T.; Peresunko, D.; Pérez Lara, C. E.; Perini, D.; Perrino, D.; Peryt, W.; Pesci, A.; Peskov, V.; Pestov, Y.; Peters, A. J.; Petráček, V.; Petran, M.; Petris, M.; Petrov, P.; Petrovici, M.; Petta, C.; Piano, S.; Piccotti, A.; Pikna, M.; Pillot, P.; Pinazza, O.; Pinsky, L.; Pitz, N.; Piuz, F.; Piyarathna, D. B.; Platt, R.; Płoskoń, M.; Pluta, J.; Pocheptsov, T.; Pochybova, S.; Podesta-Lerma, P. L. M.; Poghosyan, M. G.; Polák, K.; Polichtchouk, B.; Pop, A.; Porteboeuf, S.; Pospíšil, V.; Potukuchi, B.; Prasad, S. K.; Preghenella, R.; Prino, F.; Pruneau, C. A.; Pshenichnov, I.; Puddu, G.; Pulvirenti, A.; Punin, V.; Putiš, M.; Putschke, J.; Quercigh, E.; Qvigstad, H.; Rachevski, A.; Rademakers, A.; Rademakers, O.; Radomski, S.; Räihä, T. S.; Rak, J.; Rakotozafindrabe, A.; Ramello, L.; Ramírez Reyes, A.; Rammler, M.; Raniwala, R.; Raniwala, S.; Räsänen, S. S.; Read, K. F.; Real, J.; Redlich, K.; Renfordt, R.; Reolon, A. R.; Reshetin, A.; Rettig, F.; Revol, J.-P.; Reygers, K.; Ricaud, H.; Riccati, L.; Ricci, R. A.; Richter, M.; Riedler, P.; Riegler, W.; Riggi, F.; Rodríguez Cahuantzi, M.; Rohr, D.; Röhrich, D.; Romita, R.; Ronchetti, F.; Rosinský, P.; Rosnet, P.; Rossegger, S.; Rossi, A.; Roukoutakis, F.; Rousseau, S.; Roy, C.; Roy, P.; Rubio Montero, A. J.; Rui, R.; Rivetti, A.; Rusanov, I.; Ryabinkin, E.; Rybicki, A.; Sadovsky, S.; Šafařík, K.; Sahoo, R.; Sahu, P. K.; Saini, J.; Saiz, P.; Sakai, S.; Sakata, D.; Salgado, C. A.; Samanta, T.; Sambyal, S.; Samsonov, V.; Sanchez Castro, X.; Šándor, L.; Sandoval, A.; Sano, M.; Sano, S.; Santo, R.; Santoro, R.; Sarkamo, J.; Saturnini, P.; Scapparone, E.; Scarlassara, F.; Scharenberg, R. P.; Schiaua, C.; Schicker, R.; Schmidt, C.; Schmidt, H. R.; Schreiner, S.; Schuchmann, S.; Schukraft, J.; Schutz, Y.; Schwarz, K.; Schweda, K.; Scioli, G.; Scomparin, E.; Scott, P. A.; Scott, R.; Segato, G.; Selyuzhenkov, I.; Senyukov, S.; Seo, J.; Serci, S.; Serradilla, E.; Sevcenco, A.; Sgura, I.; Shabratova, G.; Shahoyan, R.; Sharma, N.; Sharma, S.; Shigaki, K.; Shimomura, M.; Shtejer, K.; Sibiriak, Y.; Siciliano, M.; Sicking, E.; Siemiarczuk, T.; Silenzi, A.; Silvermyr, D.; Simonetti, G.; Singaraju, R.; Singh, R.; Singhal, V.; Sinha, B. C.; Sinha, T.; Sitar, B.; Sitta, M.; Skaali, T. B.; Skjerdal, K.; Smakal, R.; Smirnov, N.; Snellings, R.; Søgaard, C.; Soloviev, A.; Soltz, R.; Son, H.; Song, J.; Song, M.; Soos, C.; Soramel, F.; Spyropoulou-Stassinaki, M.; Srivastava, B. K.; Stachel, J.; Stan, I.; Stefanek, G.; Stefanini, G.; Steinbeck, T.; Steinpreis, M.; Stenlund, E.; Steyn, G.; Stocco, D.; Stock, R.; Stokkevag, C. H.; Stolpovskiy, M.; Strmen, P.; Suaide, A. A. P.; Subieta Vásquez, M. A.; Sugitate, T.; Suire, C.; Sukhorukov, M.; Šumbera, M.; Susa, T.; Swoboda, D.; Symons, T. J. M.; Szanto de Toledo, A.; Szarka, I.; Szostak, A.; Tagridis, C.; Takahashi, J.; Tapia Takaki, J. D.; Tauro, A.; Tavlet, M.; Tejeda Muñoz, G.; Telesca, A.; Terrevoli, C.; Thäder, J.; Thomas, D.; Thomas, J. H.; Tieulent, R.; Timmins, A. R.; Tlusty, D.; Toia, A.; Torii, H.; Toscano, L.; Tosello, F.; Traczyk, T.; Truesdale, D.; Trzaska, W. H.; Tsuji, T.; Tumkin, A.; Turrisi, R.; Turvey, A. J.; Tveter, T. S.; Ulery, J.; Ullaland, K.; Uras, A.; Urbán, J.; Urciuoli, G. M.; Usai, G. L.; Vacchi, A.; Vajzer, M.; Vala, M.; Valencia Palomo, L.; Vallero, S.; van der Kolk, N.; van Leeuwen, M.; Vande Vyvre, P.; Vannucci, L.; Vargas, A.; Varma, R.; Vasileiou, M.; Vasiliev, A.; Vechernin, V.; Veldhoen, M.; Venaruzzo, M.; Vercellin, E.; Vergara, S.; Vernekohl, D. C.; Vernet, R.; Verweij, M.; Vickovic, L.; Viesti, G.; Vikhlyantsev, O.; Vilakazi, Z.; Villalobos Baillie, O.; Vinogradov, A.; Vinogradov, L.; Vinogradov, Y.; Virgili, T.; Viyogi, Y. P.; Vodopyanov, A.; Voloshin, K.; Voloshin, S.; Volpe, G.; von Haller, B.; Vranic, D.; Øvrebekk, G.; Vrláková, J.; Vulpescu, B.; Vyushin, A.; Wagner, B.; Wagner, V.; Wan, R.; Wang, D.; Wang, Y.; Wang, Y.; Watanabe, K.; Wessels, J. P.; Westerhoff, U.; Wiechula, J.; Wikne, J.; Wilde, M.; Wilk, A.; Wilk, G.; Williams, M. C. S.; Windelband, B.; Xaplanteris Karampatsos, L.; Yang, H.; Yang, S.; Yasnopolskiy, S.; Yi, J.; Yin, Z.; Yokoyama, H.; Yoo, I.-K.; Yu, W.; Yuan, X.; Yushmanov, I.; Zabrodin, E.; Zach, C.; Zampolli, C.; Zaporozhets, S.; Zarochentsev, A.; Závada, P.; Zaviyalov, N.; Zbroszczyk, H.; Zelnicek, P.; Zenin, A.; Zgura, I.; Zhalov, M.; Zhang, X.; Zhou, D.; Zichichi, A.; Zinovjev, G.; Zoccarato, Y.; Zynovyev, M.

2010-12-01

The first measurement of the charged-particle multiplicity density at midrapidity in Pb-Pb collisions at a center-of-mass energy per nucleon pair sNN=2.76TeV is presented. For an event sample corresponding to the most central 5% of the hadronic cross section, the pseudorapidity density of primary charged particles at midrapidity is 1584±4(stat)±76(syst), which corresponds to 8.3±0.4(syst) per participating nucleon pair. This represents an increase of about a factor 1.9 relative to pp collisions at similar collision energies, and about a factor 2.2 to central Au-Au collisions at sNN=0.2TeV. This measurement provides the first experimental constraint for models of nucleus-nucleus collisions at LHC energies.

Quantitative determination of pairing interactions for high-temperature superconductivity in cuprates

PubMed Central

Bok, Jin Mo; Bae, Jong Ju; Choi, Han-Yong; Varma, Chandra M.; Zhang, Wentao; He, Junfeng; Zhang, Yuxiao; Yu, Li; Zhou, X. J.

2016-01-01

A profound problem in modern condensed matter physics is discovering and understanding the nature of fluctuations and their coupling to fermions in cuprates, which lead to high-temperature superconductivity and the invariably associated strange metal state. We report the quantitative determination of normal and pairing self-energies, made possible by laser-based angle-resolved photoemission measurements of unprecedented accuracy and stability. Through a precise inversion procedure, both the effective interactions in the attractive d-wave symmetry and the repulsive part in the full symmetry are determined. The latter is nearly angle-independent. Near Tc, both interactions are nearly independent of frequency and have almost the same magnitude over the complete energy range of up to about 0.4 eV, except for a low-energy feature at around 50 meV that is present only in the repulsive part, which has less than 10% of the total spectral weight. Well below Tc, they both change similarly, with superconductivity-induced features at low energies. Besides finding the pairing self-energy and the attractive interactions for the first time, these results expose the central paradox of the problem of high Tc: how the same frequency-independent fluctuations can dominantly scatter at angles ±π/2 in the attractive channel to give d-wave pairing and lead to angle-independent repulsive scattering. The experimental results are compared with available theoretical calculations based on antiferromagnetic fluctuations, the Hubbard model, and quantum-critical fluctuations of the loop-current order. PMID:26973872

ERP evidence for memory and predictive mechanisms in word-to-text integration

PubMed Central

Stafura, Joseph Z.; Rickles, Benjamin; Perfetti, Charles A.

2016-01-01

During reading, word-to-text integration processes proceed quickly and incrementally through both prospective (predictive) and retrospective (memory) processes. Across a sentence boundary, where prediction may be less functional, memorial processes may be especially important. We tested predictive and memory mechanisms with event-related potentials (ERPs) recorded on the first content word across a sentence boundary by manipulating the direction of association between this word and one from the preceding sentence. For comparison with this text comprehension (TC) task, we tested these same word pairs in a word meaning judgment (MJ) task. In both tasks we found reduced N400 amplitudes over central scalp electrodes when the two words were either forward-associated (FA) or backward-associated (BA), relative to task-specific baseline conditions. In the MJ task, FA pairs produced a greater reduction in the N400 reduction than BA pairs over right parietal areas. However, in the TC task, BA pairs produced a greater N400 reduction than FA pairs over left parietal electrodes. A temporal principal component analysis of TC and MJ data showed a component reflecting the central N400. Additional components from TC data reflected FA-BA differences during early (N200) and late (parietal N400 and LPC) phases of processing. Comprehension skill predicted association effects in the MJ task, especially FA, and the BA central N400 effects in the TC task. The results demonstrate that, beyond N400 indicators of prediction effects, ERPs reflect the role of memory processes in word-to-text integration across sentences, part of a dynamic interplay between anticipatory and memorial processes that support comprehension. PMID:27110578

A short walk in quantum probability

NASA Astrophysics Data System (ADS)

Hudson, Robin

2018-04-01

This is a personal survey of aspects of quantum probability related to the Heisenberg commutation relation for canonical pairs. Using the failure, in general, of non-negativity of the Wigner distribution for canonical pairs to motivate a more satisfactory quantum notion of joint distribution, we visit a central limit theorem for such pairs and a resulting family of quantum planar Brownian motions which deform the classical planar Brownian motion, together with a corresponding family of quantum stochastic areas. This article is part of the themed issue `Hilbert's sixth problem'.

Quantum information processing in the radical-pair mechanism: Haberkorn's theory violates the Ozawa entropy bound

NASA Astrophysics Data System (ADS)

Mouloudakis, K.; Kominis, I. K.

2017-02-01

Radical-ion-pair reactions, central for understanding the avian magnetic compass and spin transport in photosynthetic reaction centers, were recently shown to be a fruitful paradigm of the new synthesis of quantum information science with biological processes. We show here that the master equation so far constituting the theoretical foundation of spin chemistry violates fundamental bounds for the entropy of quantum systems, in particular the Ozawa bound. In contrast, a recently developed theory based on quantum measurements, quantum coherence measures, and quantum retrodiction, thus exemplifying the paradigm of quantum biology, satisfies the Ozawa bound as well as the Lanford-Robinson bound on information extraction. By considering Groenewold's information, the quantum information extracted during the reaction, we reproduce the known and unravel other magnetic-field effects not conveyed by reaction yields.

Femtoscopy with identified charged pions in proton-lead collisions at s NN = 5.02 TeV with ATLAS

DOE PAGES

Aaboud, M.; Aad, G.; Abbott, B.; ...

2017-12-28

Bose-Einsmore » tein correlations between identified charged pions are measured for p+Pb collisions at s NN =5.02 TeV using data recorded by the ATLAS detector at the CERN Large Hadron Collider corresponding to a total integrated luminosity of 28nb-1. Pions are identified using ionization energy loss measured in the pixel detector. Two-particle correlation functions and the extracted source radii are presented as a function of collision centrality as well as the average transverse momentum (kT) and rapidity (yππ) of the pair. Pairs are selected with a rapidity -2 < yππ < 1 and with an average transverse momentum 0.1 < kT < 0.8GeV. The effect of jet fragmentation on the two-particle correlation function is studied, and a method using opposite-charge pair data to constrain its contributions to the measured correlations is described. The measured source sizes are substantially larger in more central collisions and are observed to decrease with increasing pair kT. A correlation of the radii with the local charged-particle density is demonstrated. The scaling of the extracted radii with the mean number of participating nucleons is also used to compare a selection of initial-geometry models. The cross term Rol is measured as a function of rapidity, and a nonzero value is observed with 5.1σ combined significance for -1 < yππ < 1 in the most central events.« less

Femtoscopy with identified charged pions in proton-lead collisions at s NN = 5.02 TeV with ATLAS

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

Aaboud, M.; Aad, G.; Abbott, B.

Bose-Einsmore » tein correlations between identified charged pions are measured for p+Pb collisions at s NN =5.02 TeV using data recorded by the ATLAS detector at the CERN Large Hadron Collider corresponding to a total integrated luminosity of 28nb-1. Pions are identified using ionization energy loss measured in the pixel detector. Two-particle correlation functions and the extracted source radii are presented as a function of collision centrality as well as the average transverse momentum (kT) and rapidity (yππ) of the pair. Pairs are selected with a rapidity -2 < yππ < 1 and with an average transverse momentum 0.1 < kT < 0.8GeV. The effect of jet fragmentation on the two-particle correlation function is studied, and a method using opposite-charge pair data to constrain its contributions to the measured correlations is described. The measured source sizes are substantially larger in more central collisions and are observed to decrease with increasing pair kT. A correlation of the radii with the local charged-particle density is demonstrated. The scaling of the extracted radii with the mean number of participating nucleons is also used to compare a selection of initial-geometry models. The cross term Rol is measured as a function of rapidity, and a nonzero value is observed with 5.1σ combined significance for -1 < yππ < 1 in the most central events.« less

Femtoscopy with identified charged pions in proton-lead collisions at √{sNN}=5.02 TeV with ATLAS

NASA Astrophysics Data System (ADS)

Aaboud, M.; Aad, G.; Abbott, B.; Abdallah, J.; Abdinov, O.; Abeloos, B.; Aben, R.; Abouzeid, O. S.; Abraham, N. L.; Abramowicz, H.; Abreu, H.; Abreu, R.; Abulaiti, Y.; Acharya, B. S.; Adamczyk, L.; Adams, D. L.; Adelman, J.; Adomeit, S.; Adye, T.; Affolder, A. A.; Agatonovic-Jovin, T.; Agricola, J.; Aguilar-Saavedra, J. A.; Ahlen, S. P.; Ahmadov, F.; Aielli, G.; Akerstedt, H.; Åkesson, T. P. A.; Akimov, A. V.; Alberghi, G. L.; Albert, J.; Albrand, S.; Alconadaâ Verzini, M. J.; Aleksa, M.; Aleksandrov, I. N.; Alexa, C.; Alexander, G.; Alexopoulos, T.; Alhroob, M.; Ali, B.; Aliev, M.; Alimonti, G.; Alison, J.; Alkire, S. P.; Allbrooke, B. M. M.; Allen, B. W.; Allport, P. P.; Aloisio, A.; Alonso, A.; Alonso, F.; Alpigiani, C.; Alshehri, A. A.; Alstaty, M.; Alvarezâ Gonzalez, B.; Álvarezâ Piqueras, D.; Alviggi, M. G.; Amadio, B. T.; Amako, K.; Amaralâ Coutinho, Y.; Amelung, C.; Amidei, D.; Amorâ Dosâ Santos, S. P.; Amorim, A.; Amoroso, S.; Amundsen, G.; Anastopoulos, C.; Ancu, L. S.; Andari, N.; Andeen, T.; Anders, C. F.; Anders, G.; Anders, J. K.; Anderson, K. J.; Andreazza, A.; Andrei, V.; Angelidakis, S.; Angelozzi, I.; Anger, P.; Angerami, A.; Anghinolfi, F.; Anisenkov, A. V.; Anjos, N.; Annovi, A.; Antel, C.; Antonelli, M.; Antonov, A.; Anulli, F.; Aoki, M.; Aperioâ Bella, L.; Arabidze, G.; Arai, Y.; Araque, J. P.; Arce, A. T. H.; Arduh, F. A.; Arguin, J.-F.; Argyropoulos, S.; Arik, M.; Armbruster, A. J.; Armitage, L. J.; Arnaez, O.; Arnold, H.; Arratia, M.; Arslan, O.; Artamonov, A.; Artoni, G.; Artz, S.; Asai, S.; Asbah, N.; Ashkenazi, A.; Åsman, B.; Asquith, L.; Assamagan, K.; Astalos, R.; Atkinson, M.; Atlay, N. B.; Augsten, K.; Avolio, G.; Axen, B.; Ayoub, M. K.; Azuelos, G.; Baak, M. A.; Baas, A. E.; Baca, M. J.; Bachacou, H.; Bachas, K.; Backes, M.; Backhaus, M.; Bagiacchi, P.; Bagnaia, P.; Bai, Y.; Baines, J. T.; Baker, O. K.; Baldin, E. M.; Balek, P.; Balestri, T.; Balli, F.; Balunas, W. K.; Banas, E.; Banerjee, Sw.; Bannoura, A. A. E.; Barak, L.; Barberio, E. L.; Barberis, D.; Barbero, M.; Barillari, T.; Barisits, M.-S.; Barklow, T.; Barlow, N.; Barnes, S. L.; Barnett, B. M.; Barnett, R. M.; Barnovska-Blenessy, Z.; Baroncelli, A.; Barone, G.; Barr, A. J.; Barrancoâ Navarro, L.; Barreiro, F.; Barreiroâ Guimarãesâ Daâ Costa, J.; Bartoldus, R.; Barton, A. E.; Bartos, P.; Basalaev, A.; Bassalat, A.; Bates, R. L.; Batista, S. J.; Batley, J. R.; Battaglia, M.; Bauce, M.; Bauer, F.; Bawa, H. S.; Beacham, J. B.; Beattie, M. D.; Beau, T.; Beauchemin, P. H.; Bechtle, P.; Beck, H. P.; Becker, K.; Becker, M.; Beckingham, M.; Becot, C.; Beddall, A. J.; Beddall, A.; Bednyakov, V. A.; Bedognetti, M.; Bee, C. P.; Beemster, L. J.; Beermann, T. A.; Begel, M.; Behr, J. K.; Belanger-Champagne, C.; Bell, A. S.; Bella, G.; Bellagamba, L.; Bellerive, A.; Bellomo, M.; Belotskiy, K.; Beltramello, O.; Belyaev, N. L.; Benary, O.; Benchekroun, D.; Bender, M.; Bendtz, K.; Benekos, N.; Benhammou, Y.; Benharâ Noccioli, E.; Benitez, J.; Benjamin, D. P.; Bensinger, J. R.; Bentvelsen, S.; Beresford, L.; Beretta, M.; Berge, D.; Bergeaasâ Kuutmann, E.; Berger, N.; Beringer, J.; Berlendis, S.; Bernard, N. R.; Bernius, C.; Bernlochner, F. U.; Berry, T.; Berta, P.; Bertella, C.; Bertoli, G.; Bertolucci, F.; Bertram, I. A.; Bertsche, C.; Bertsche, D.; Besjes, G. J.; Bessidskaiaâ Bylund, O.; Bessner, M.; Besson, N.; Betancourt, C.; Bethani, A.; Bethke, S.; Bevan, A. J.; Bianchi, R. M.; Bianchini, L.; Bianco, M.; Biebel, O.; Biedermann, D.; Bielski, R.; Biesuz, N. V.; Biglietti, M.; Bilbaoâ Deâ Mendizabal, J.; Billoud, T. R. V.; Bilokon, H.; Bindi, M.; Binet, S.; Bingul, A.; Bini, C.; Biondi, S.; Bisanz, T.; Bjergaard, D. M.; Black, C. W.; Black, J. E.; Black, K. M.; Blackburn, D.; Blair, R. E.; Blanchard, J.-B.; Blazek, T.; Bloch, I.; Blocker, C.; Blue, A.; Blum, W.; Blumenschein, U.; Blunier, S.; Bobbink, G. J.; Bobrovnikov, V. S.; Bocchetta, S. S.; Bocci, A.; Bock, C.; Boehler, M.; Boerner, D.; Bogaerts, J. A.; Bogavac, D.; Bogdanchikov, A. G.; Bohm, C.; Boisvert, V.; Bokan, P.; Bold, T.; Boldyrev, A. S.; Bomben, M.; Bona, M.; Boonekamp, M.; Borisov, A.; Borissov, G.; Bortfeldt, J.; Bortoletto, D.; Bortolotto, V.; Boscherini, D.; Bosman, M.; Bossioâ Sola, J. D.; Boudreau, J.; Bouffard, J.; Bouhova-Thacker, E. V.; Boumediene, D.; Bourdarios, C.; Boutle, S. K.; Boveia, A.; Boyd, J.; Boyko, I. R.; Bracinik, J.; Brandt, A.; Brandt, G.; Brandt, O.; Bratzler, U.; Brau, B.; Brau, J. E.; Braun, H. M.; Breadenâ Madden, W. D.; Brendlinger, K.; Brennan, A. J.; Brenner, L.; Brenner, R.; Bressler, S.; Bristow, T. M.; Britton, D.; Britzger, D.; Brochu, F. M.; Brock, I.; Brock, R.; Brooijmans, G.; Brooks, T.; Brooks, W. K.; Brosamer, J.; Brost, E.; Broughton, J. H.; Bruckmanâ Deâ Renstrom, P. A.; Bruncko, D.; Bruneliere, R.; Bruni, A.; Bruni, G.; Bruni, L. S.; Brunt, Bh; Bruschi, M.; Bruscino, N.; Bryant, P.; Bryngemark, L.; Buanes, T.; Buat, Q.; Buchholz, P.; Buckley, A. G.; Budagov, I. A.; Buehrer, F.; Bugge, M. K.; Bulekov, O.; Bullock, D.; Burckhart, H.; Burdin, S.; Burgard, C. D.; Burghgrave, B.; Burka, K.; Burke, S.; Burmeister, I.; Burr, J. T. P.; Busato, E.; Büscher, D.; Büscher, V.; Bussey, P.; Butler, J. M.; Buttar, C. M.; Butterworth, J. M.; Butti, P.; Buttinger, W.; Buzatu, A.; Buzykaev, A. R.; Cabreraâ Urbán, S.; Caforio, D.; Cairo, V. M.; Cakir, O.; Calace, N.; Calafiura, P.; Calandri, A.; Calderini, G.; Calfayan, P.; Callea, G.; Caloba, L. P.; Calventeâ Lopez, S.; Calvet, D.; Calvet, S.; Calvet, T. P.; Camachoâ Toro, R.; Camarda, S.; Camarri, P.; Cameron, D.; Caminalâ Armadans, R.; Camincher, C.; Campana, S.; Campanelli, M.; Camplani, A.; Campoverde, A.; Canale, V.; Canepa, A.; Canoâ Bret, M.; Cantero, J.; Cao, T.; Capeansâ Garrido, M. D. M.; Caprini, I.; Caprini, M.; Capua, M.; Carbone, R. M.; Cardarelli, R.; Cardillo, F.; Carli, I.; Carli, T.; Carlino, G.; Carminati, L.; Caron, S.; Carquin, E.; Carrillo-Montoya, G. D.; Carter, J. R.; Carvalho, J.; Casadei, D.; Casado, M. P.; Casolino, M.; Casper, D. W.; Castaneda-Miranda, E.; Castelijn, R.; Castelli, A.; Castilloâ Gimenez, V.; Castro, N. F.; Catinaccio, A.; Catmore, J. R.; Cattai, A.; Caudron, J.; Cavaliere, V.; Cavallaro, E.; Cavalli, D.; Cavalli-Sforza, M.; Cavasinni, V.; Ceradini, F.; Cerdaâ Alberich, L.; Cerio, B. C.; Cerqueira, A. S.; Cerri, A.; Cerrito, L.; Cerutti, F.; Cerv, M.; Cervelli, A.; Cetin, S. A.; Chafaq, A.; Chakraborty, D.; Chan, S. K.; Chan, Y. L.; Chang, P.; Chapman, J. D.; Charlton, D. G.; Chatterjee, A.; Chau, C. C.; Chavezâ Barajas, C. A.; Che, S.; Cheatham, S.; Chegwidden, A.; Chekanov, S.; Chekulaev, S. V.; Chelkov, G. A.; Chelstowska, M. A.; Chen, C.; Chen, H.; Chen, K.; Chen, S.; Chen, S.; Chen, X.; Chen, Y.; Cheng, H. C.; Cheng, H. J.; Cheng, Y.; Cheplakov, A.; Cheremushkina, E.; Cherkaouiâ Elâ Moursli, R.; Chernyatin, V.; Cheu, E.; Chevalier, L.; Chiarella, V.; Chiarelli, G.; Chiodini, G.; Chisholm, A. S.; Chitan, A.; Chizhov, M. V.; Choi, K.; Chomont, A. R.; Chouridou, S.; Chow, B. K. B.; Christodoulou, V.; Chromek-Burckhart, D.; Chudoba, J.; Chuinard, A. J.; Chwastowski, J. J.; Chytka, L.; Ciapetti, G.; Ciftci, A. K.; Cinca, D.; Cindro, V.; Cioara, I. A.; Ciocca, C.; Ciocio, A.; Cirotto, F.; Citron, Z. H.; Citterio, M.; Ciubancan, M.; Clark, A.; Clark, B. L.; Clark, M. R.; Clark, P. J.; Clarke, R. N.; Clement, C.; Coadou, Y.; Cobal, M.; Coccaro, A.; Cochran, J.; Colasurdo, L.; Cole, B.; Colijn, A. P.; Collot, J.; Colombo, T.; Compostella, G.; Condeâ Muiño, P.; Coniavitis, E.; Connell, S. H.; Connelly, I. A.; Consorti, V.; Constantinescu, S.; Conti, G.; Conventi, F.; Cooke, M.; Cooper, B. D.; Cooper-Sarkar, A. M.; Cormier, K. J. R.; Cornelissen, T.; Corradi, M.; Corriveau, F.; Corso-Radu, A.; Cortes-Gonzalez, A.; Cortiana, G.; Costa, G.; Costa, M. J.; Costanzo, D.; Cottin, G.; Cowan, G.; Cox, B. E.; Cranmer, K.; Crawley, S. J.; Cree, G.; Crépé-Renaudin, S.; Crescioli, F.; Cribbs, W. A.; Crispinâ Ortuzar, M.; Cristinziani, M.; Croft, V.; Crosetti, G.; Cueto, A.; Cuhadarâ Donszelmann, T.; Cummings, J.; Curatolo, M.; Cúth, J.; Czirr, H.; Czodrowski, P.; D'Amen, G.; D'Auria, S.; D'Onofrio, M.; Daâ Cunhaâ Sargedasâ Deâ Sousa, M. J.; Daâ Via, C.; Dabrowski, W.; Dado, T.; Dai, T.; Dale, O.; Dallaire, F.; Dallapiccola, C.; Dam, M.; Dandoy, J. R.; Dang, N. P.; Daniells, A. C.; Dann, N. S.; Danninger, M.; Danoâ Hoffmann, M.; Dao, V.; Darbo, G.; Darmora, S.; Dassoulas, J.; Dattagupta, A.; Davey, W.; David, C.; Davidek, T.; Davies, M.; Davison, P.; Dawe, E.; Dawson, I.; de, K.; Deâ Asmundis, R.; Deâ Benedetti, A.; Deâ Castro, S.; Deâ Cecco, S.; Deâ Groot, N.; Deâ Jong, P.; Deâ Laâ Torre, H.; Deâ Lorenzi, F.; Deâ Maria, A.; Deâ Pedis, D.; Deâ Salvo, A.; Deâ Sanctis, U.; Deâ Santo, A.; Deâ Vivieâ Deâ Regie, J. B.; Dearnaley, W. J.; Debbe, R.; Debenedetti, C.; Dedovich, D. V.; Dehghanian, N.; Deigaard, I.; Delâ Gaudio, M.; Delâ Peso, J.; Delâ Prete, T.; Delgove, D.; Deliot, F.; Delitzsch, C. M.; Dell'Acqua, A.; Dell'Asta, L.; Dell'Orso, M.; Dellaâ Pietra, M.; Dellaâ Volpe, D.; Delmastro, M.; Delsart, P. A.; Demarco, D. A.; Demers, S.; Demichev, M.; Demilly, A.; Denisov, S. P.; Denysiuk, D.; Derendarz, D.; Derkaoui, J. E.; Derue, F.; Dervan, P.; Desch, K.; Deterre, C.; Dette, K.; Deviveiros, P. O.; Dewhurst, A.; Dhaliwal, S.; Diâ Ciaccio, A.; Diâ Ciaccio, L.; Diâ Clemente, W. K.; Diâ Donato, C.; Diâ Girolamo, A.; Diâ Girolamo, B.; Diâ Micco, B.; Diâ Nardo, R.; Diâ Simone, A.; Diâ Sipio, R.; Diâ Valentino, D.; Diaconu, C.; Diamond, M.; Dias, F. A.; Diaz, M. A.; Diehl, E. B.; Dietrich, J.; Díezâ Cornell, S.; Dimitrievska, A.; Dingfelder, J.; Dita, P.; Dita, S.; Dittus, F.; Djama, F.; Djobava, T.; Djuvsland, J. I.; Doâ Vale, M. A. B.; Dobos, D.; Dobre, M.; Doglioni, C.; Dolejsi, J.; Dolezal, Z.; Donadelli, M.; Donati, S.; Dondero, P.; Donini, J.; Dopke, J.; Doria, A.; Dova, M. T.; Doyle, A. T.; Drechsler, E.; Dris, M.; Du, Y.; Duarte-Campderros, J.; Duchovni, E.; Duckeck, G.; Ducu, O. A.; Duda, D.; Dudarev, A.; Dudder, A. Chr.; Duffield, E. M.; Duflot, L.; Dührssen, M.; Dumancic, M.; Dunford, M.; Duranâ Yildiz, H.; Düren, M.; Durglishvili, A.; Duschinger, D.; Dutta, B.; Dyndal, M.; Eckardt, C.; Ecker, K. M.; Edgar, R. C.; Edwards, N. C.; Eifert, T.; Eigen, G.; Einsweiler, K.; Ekelof, T.; Elâ Kacimi, M.; Ellajosyula, V.; Ellert, M.; Elles, S.; Ellinghaus, F.; Elliot, A. A.; Ellis, N.; Elmsheuser, J.; Elsing, M.; Emeliyanov, D.; Enari, Y.; Endner, O. C.; Ennis, J. S.; Erdmann, J.; Ereditato, A.; Ernis, G.; Ernst, J.; Ernst, M.; Errede, S.; Ertel, E.; Escalier, M.; Esch, H.; Escobar, C.; Esposito, B.; Etienvre, A. I.; Etzion, E.; Evans, H.; Ezhilov, A.; Fabbri, F.; Fabbri, L.; Facini, G.; Fakhrutdinov, R. M.; Falciano, S.; Falla, R. J.; Faltova, J.; Fang, Y.; Fanti, M.; Farbin, A.; Farilla, A.; Farina, C.; Farina, E. M.; Farooque, T.; Farrell, S.; Farrington, S. M.; Farthouat, P.; Fassi, F.; Fassnacht, P.; Fassouliotis, D.; Faucciâ Giannelli, M.; Favareto, A.; Fawcett, W. J.; Fayard, L.; Fedin, O. L.; Fedorko, W.; Feigl, S.; Feligioni, L.; Feng, C.; Feng, E. J.; Feng, H.; Fenyuk, A. B.; Feremenga, L.; Fernandezâ Martinez, P.; Fernandezâ Perez, S.; Ferrando, J.; Ferrari, A.; Ferrari, P.; Ferrari, R.; Ferreiraâ Deâ Lima, D. E.; Ferrer, A.; Ferrere, D.; Ferretti, C.; Ferrettoâ Parodi, A.; Fiedler, F.; Filipčič, A.; Filipuzzi, M.; Filthaut, F.; Fincke-Keeler, M.; Finelli, K. D.; Fiolhais, M. C. N.; Fiorini, L.; Firan, A.; Fischer, A.; Fischer, C.; Fischer, J.; Fisher, W. C.; Flaschel, N.; Fleck, I.; Fleischmann, P.; Fletcher, G. T.; Fletcher, R. R. M.; Flick, T.; Floderus, A.; Floresâ Castillo, L. R.; Flowerdew, M. J.; Forcolin, G. T.; Formica, A.; Forti, A.; Foster, A. G.; Fournier, D.; Fox, H.; Fracchia, S.; Francavilla, P.; Franchini, M.; Francis, D.; Franconi, L.; Franklin, M.; Frate, M.; Fraternali, M.; Freeborn, D.; Fressard-Batraneanu, S. M.; Friedrich, F.; Froidevaux, D.; Frost, J. A.; Fukunaga, C.; Fullanaâ Torregrosa, E.; Fusayasu, T.; Fuster, J.; Gabaldon, C.; Gabizon, O.; Gabrielli, A.; Gabrielli, A.; Gach, G. P.; Gadatsch, S.; Gadomski, S.; Gagliardi, G.; Gagnon, L. G.; Gagnon, P.; Galea, C.; Galhardo, B.; Gallas, E. J.; Gallop, B. J.; Gallus, P.; Galster, G.; Gan, K. K.; Gao, J.; Gao, Y.; Gao, Y. S.; Garayâ Walls, F. M.; García, C.; Garcíaâ Navarro, J. E.; Garcia-Sciveres, M.; Gardner, R. W.; Garelli, N.; Garonne, V.; Gasconâ Bravo, A.; Gasnikova, K.; Gatti, C.; Gaudiello, A.; Gaudio, G.; Gauthier, L.; Gavrilenko, I. L.; Gay, C.; Gaycken, G.; Gazis, E. N.; Gecse, Z.; Gee, C. N. P.; Geich-Gimbel, Ch.; Geisen, M.; Geisler, M. P.; Gemme, C.; Genest, M. H.; Geng, C.; Gentile, S.; Gentsos, C.; George, S.; Gerbaudo, D.; Gershon, A.; Ghasemi, S.; Ghneimat, M.; Giacobbe, B.; Giagu, S.; Giannetti, P.; Gibbard, B.; Gibson, S. M.; Gignac, M.; Gilchriese, M.; Gillam, T. P. S.; Gillberg, D.; Gilles, G.; Gingrich, D. M.; Giokaris, N.; Giordani, M. P.; Giorgi, F. M.; Giorgi, F. M.; Giraud, P. F.; Giromini, P.; Giugni, D.; Giuli, F.; Giuliani, C.; Giulini, M.; Gjelsten, B. K.; Gkaitatzis, S.; Gkialas, I.; Gkougkousis, E. L.; Gladilin, L. K.; Glasman, C.; Glatzer, J.; Glaysher, P. C. F.; Glazov, A.; Goblirsch-Kolb, M.; Godlewski, J.; Goldfarb, S.; Golling, T.; Golubkov, D.; Gomes, A.; Gonçalo, R.; Goncalvesâ Pintoâ Firminoâ Daâ Costa, J.; Gonella, G.; Gonella, L.; Gongadze, A.; Gonzálezâ Deâ Laâ Hoz, S.; Gonzalezâ Parra, G.; Gonzalez-Sevilla, S.; Goossens, L.; Gorbounov, P. A.; Gordon, H. A.; Gorelov, I.; Gorini, B.; Gorini, E.; Gorišek, A.; Gornicki, E.; Goshaw, A. T.; Gössling, C.; Gostkin, M. I.; Goudet, C. R.; Goujdami, D.; Goussiou, A. G.; Govender, N.; Gozani, E.; Graber, L.; Grabowska-Bold, I.; Gradin, P. O. J.; Grafström, P.; Gramling, J.; Gramstad, E.; Grancagnolo, S.; Gratchev, V.; Gravila, P. M.; Gray, H. M.; Graziani, E.; Greenwood, Z. D.; Grefe, C.; Gregersen, K.; Gregor, I. M.; Grenier, P.; Grevtsov, K.; Griffiths, J.; Grillo, A. A.; Grimm, K.; Grinstein, S.; Gris, Ph.; Grivaz, J.-F.; Groh, S.; Grohs, J. P.; Gross, E.; Grosse-Knetter, J.; Grossi, G. C.; Grout, Z. J.; Guan, L.; Guan, W.; Guenther, J.; Guescini, F.; Guest, D.; Gueta, O.; Guido, E.; Guillemin, T.; Guindon, S.; Gul, U.; Gumpert, C.; Guo, J.; Guo, Y.; Gupta, R.; Gupta, S.; Gustavino, G.; Gutierrez, P.; Gutierrezâ Ortiz, N. G.; Gutschow, C.; Guyot, C.; Gwenlan, C.; Gwilliam, C. B.; Haas, A.; Haber, C.; Hadavand, H. K.; Hadef, A.; Hageböck, S.; Hajduk, Z.; Hakobyan, H.; Haleem, M.; Haley, J.; Halladjian, G.; Hallewell, G. D.; Hamacher, K.; Hamal, P.; Hamano, K.; Hamilton, A.; Hamity, G. N.; Hamnett, P. G.; Han, L.; Hanagaki, K.; Hanawa, K.; Hance, M.; Haney, B.; Hanke, P.; Hanna, R.; Hansen, J. B.; Hansen, J. D.; Hansen, M. C.; Hansen, P. H.; Hara, K.; Hard, A. S.; Harenberg, T.; Hariri, F.; Harkusha, S.; Harrington, R. D.; Harrison, P. F.; Hartmann, N. M.; Hasegawa, M.; Hasegawa, Y.; Hasib, A.; Hassani, S.; Haug, S.; Hauser, R.; Hauswald, L.; Havranek, M.; Hawkes, C. M.; Hawkings, R. J.; Hayakawa, D.; Hayden, D.; Hays, C. 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L.; Reznicek, P.; Rezvani, R.; Richter, R.; Richter, S.; Richter-Was, E.; Ricken, O.; Ridel, M.; Rieck, P.; Riegel, C. J.; Rieger, J.; Rifki, O.; Rijssenbeek, M.; Rimoldi, A.; Rimoldi, M.; Rinaldi, L.; Ristić, B.; Ritsch, E.; Riu, I.; Rizatdinova, F.; Rizvi, E.; Rizzi, C.; Robertson, S. H.; Robichaud-Veronneau, A.; Robinson, D.; Robinson, J. E. M.; Robson, A.; Roda, C.; Rodina, Y.; Rodriguezâ Perez, A.; Rodriguezâ Rodriguez, D.; Roe, S.; Rogan, C. S.; Røhne, O.; Romaniouk, A.; Romano, M.; Romanoâ Saez, S. M.; Romeroâ Adam, E.; Rompotis, N.; Ronzani, M.; Roos, L.; Ros, E.; Rosati, S.; Rosbach, K.; Rose, P.; Rosien, N.-A.; Rossetti, V.; Rossi, E.; Rossi, L. P.; Rosten, J. H. N.; Rosten, R.; Rotaru, M.; Roth, I.; Rothberg, J.; Rousseau, D.; Rozanov, A.; Rozen, Y.; Ruan, X.; Rubbo, F.; Rudolph, M. S.; Rühr, F.; Ruiz-Martinez, A.; Rurikova, Z.; Rusakovich, N. A.; Ruschke, A.; Russell, H. L.; Rutherfoord, J. P.; Ruthmann, N.; Ryabov, Y. F.; Rybar, M.; Rybkin, G.; Ryu, S.; Ryzhov, A.; Rzehorz, G. F.; Saavedra, A. F.; Sabato, G.; Sacerdoti, S.; Sadrozinski, H. F.-W.; Sadykov, R.; Safaiâ Tehrani, F.; Saha, P.; Sahinsoy, M.; Saimpert, M.; Saito, T.; Sakamoto, H.; Sakurai, Y.; Salamanna, G.; Salamon, A.; Salazarâ Loyola, J. E.; Salek, D.; Salesâ Deâ Bruin, P. H.; Salihagic, D.; Salnikov, A.; Salt, J.; Salvatore, D.; Salvatore, F.; Salvucci, A.; Salzburger, A.; Sammel, D.; Sampsonidis, D.; Sánchez, J.; Sanchezâ Martinez, V.; Sanchezâ Pineda, A.; Sandaker, H.; Sandbach, R. L.; Sander, H. G.; Sandhoff, M.; Sandoval, C.; Sankey, D. P. C.; Sannino, M.; Sansoni, A.; Santoni, C.; Santonico, R.; Santos, H.; Santoyoâ Castillo, I.; Sapp, K.; Sapronov, A.; Saraiva, J. G.; Sarrazin, B.; Sasaki, O.; Sato, K.; Sauvan, E.; Savage, G.; Savard, P.; Savic, N.; Sawyer, C.; Sawyer, L.; Saxon, J.; Sbarra, C.; Sbrizzi, A.; Scanlon, T.; Scannicchio, D. A.; Scarcella, M.; Scarfone, V.; Schaarschmidt, J.; Schacht, P.; Schachtner, B. M.; Schaefer, D.; Schaefer, L.; Schaefer, R.; Schaeffer, J.; Schaepe, S.; Schaetzel, S.; Schäfer, U.; Schaffer, A. C.; Schaile, D.; Schamberger, R. D.; Scharf, V.; Schegelsky, V. A.; Scheirich, D.; Schernau, M.; Schiavi, C.; Schier, S.; Schillo, C.; Schioppa, M.; Schlenker, S.; Schmidt-Sommerfeld, K. R.; Schmieden, K.; Schmitt, C.; Schmitt, S.; Schmitz, S.; Schneider, B.; Schnoor, U.; Schoeffel, L.; Schoening, A.; Schoenrock, B. D.; Schopf, E.; Schott, M.; Schouwenberg, J. F. P.; Schovancova, J.; Schramm, S.; Schreyer, M.; Schuh, N.; Schulte, A.; Schultens, M. J.; Schultz-Coulon, H.-C.; Schulz, H.; Schumacher, M.; Schumm, B. A.; Schune, Ph.; Schwartzman, A.; Schwarz, T. A.; Schweiger, H.; Schwemling, Ph.; Schwienhorst, R.; Schwindling, J.; Schwindt, T.; Sciolla, G.; Scuri, F.; Scutti, F.; Searcy, J.; Seema, P.; Seidel, S. C.; Seiden, A.; Seifert, F.; Seixas, J. M.; Sekhniaidze, G.; Sekhon, K.; Sekula, S. J.; Seliverstov, D. M.; Semprini-Cesari, N.; Serfon, C.; Serin, L.; Serkin, L.; Sessa, M.; Seuster, R.; Severini, H.; Sfiligoj, T.; Sforza, F.; Sfyrla, A.; Shabalina, E.; Shaikh, N. W.; Shan, L. Y.; Shang, R.; Shank, J. T.; Shapiro, M.; Shatalov, P. B.; Shaw, K.; Shaw, S. M.; Shcherbakova, A.; Shehu, C. Y.; Sherwood, P.; Shi, L.; Shimizu, S.; Shimmin, C. O.; Shimojima, M.; Shiyakova, M.; Shmeleva, A.; Shoalehâ Saadi, D.; Shochet, M. J.; Shojaii, S.; Shope, D. R.; Shrestha, S.; Shulga, E.; Shupe, M. A.; Sicho, P.; Sickles, A. M.; Sidebo, P. E.; Sidiropoulou, O.; Sidorov, D.; Sidoti, A.; Siegert, F.; Sijacki, Dj.; Silva, J.; Silverstein, S. B.; Simak, V.; Simic, Lj.; Simion, S.; Simioni, E.; Simmons, B.; Simon, D.; Simon, M.; Sinervo, P.; Sinev, N. B.; Sioli, M.; Siragusa, G.; Sivoklokov, S. Yu.; Sjölin, J.; Skinner, M. B.; Skottowe, H. P.; Skubic, P.; Slater, M.; Slavicek, T.; Slawinska, M.; Sliwa, K.; Slovak, R.; Smakhtin, V.; Smart, B. H.; Smestad, L.; Smiesko, J.; Smirnov, S. Yu.; Smirnov, Y.; Smirnova, L. N.; Smirnova, O.; Smith, M. N. K.; Smith, R. W.; Smizanska, M.; Smolek, K.; Snesarev, A. A.; Snyder, S.; Sobie, R.; Socher, F.; Soffer, A.; Soh, D. A.; Sokhrannyi, G.; Solansâ Sanchez, C. A.; Solar, M.; Soldatov, E. Yu.; Soldevila, U.; Solodkov, A. A.; Soloshenko, A.; Solovyanov, O. V.; Solovyev, V.; Sommer, P.; Son, H.; Song, H. Y.; Sood, A.; Sopczak, A.; Sopko, V.; Sorin, V.; Sosa, D.; Sotiropoulou, C. L.; Soualah, R.; Soukharev, A. M.; South, D.; Sowden, B. C.; Spagnolo, S.; Spalla, M.; Spangenberg, M.; Spanò, F.; Sperlich, D.; Spettel, F.; Spighi, R.; Spigo, G.; Spiller, L. A.; Spousta, M.; St. Denis, R. D.; Stabile, A.; Stamen, R.; Stamm, S.; Stanecka, E.; Stanek, R. W.; Stanescu, C.; Stanescu-Bellu, M.; Stanitzki, M. M.; Stapnes, S.; Starchenko, E. A.; Stark, G. H.; Stark, J.; Stark, S. H.; Staroba, P.; Starovoitov, P.; Stärz, S.; Staszewski, R.; Steinberg, P.; Stelzer, B.; Stelzer, H. J.; Stelzer-Chilton, O.; Stenzel, H.; Stewart, G. A.; Stillings, J. A.; Stockton, M. C.; Stoebe, M.; Stoicea, G.; Stolte, P.; Stonjek, S.; Stradling, A. R.; Straessner, A.; Stramaglia, M. E.; Strandberg, J.; Strandberg, S.; Strandlie, A.; Strauss, M.; Strizenec, P.; Ströhmer, R.; Strom, D. M.; Stroynowski, R.; Strubig, A.; Stucci, S. A.; Stugu, B.; Styles, N. A.; Su, D.; Su, J.; Suchek, S.; Sugaya, Y.; Suk, M.; Sulin, V. V.; Sultansoy, S.; Sumida, T.; Sun, S.; Sun, X.; Sundermann, J. E.; Suruliz, K.; Susinno, G.; Sutton, M. R.; Suzuki, S.; Svatos, M.; Swiatlowski, M.; Sykora, I.; Sykora, T.; Ta, D.; Taccini, C.; Tackmann, K.; Taenzer, J.; Taffard, A.; Tafirout, R.; Taiblum, N.; Takai, H.; Takashima, R.; Takeshita, T.; Takubo, Y.; Talby, M.; Talyshev, A. A.; Tan, K. G.; Tanaka, J.; Tanaka, M.; Tanaka, R.; Tanaka, S.; Tanioka, R.; Tannenwald, B. B.; Tapiaâ Araya, S.; Tapprogge, S.; Tarem, S.; Tartarelli, G. F.; Tas, P.; Tasevsky, M.; Tashiro, T.; Tassi, E.; Tavaresâ Delgado, A.; Tayalati, Y.; Taylor, A. C.; Taylor, G. N.; Taylor, P. T. E.; Taylor, W.; Teischinger, F. A.; Teixeira-Dias, P.; Temple, D.; Tenâ Kate, H.; Teng, P. K.; Teoh, J. J.; Tepel, F.; Terada, S.; Terashi, K.; Terron, J.; Terzo, S.; Testa, M.; Teuscher, R. J.; Theveneaux-Pelzer, T.; Thomas, J. P.; Thomas-Wilsker, J.; Thompson, E. N.; Thompson, P. D.; Thompson, A. S.; Thomsen, L. A.; Thomson, E.; Thomson, M.; Tibbetts, M. J.; Ticseâ Torres, R. E.; Tikhomirov, V. O.; Tikhonov, Yu. A.; Timoshenko, S.; Tipton, P.; Tisserant, S.; Todome, K.; Todorov, T.; Todorova-Nova, S.; Tojo, J.; Tokár, S.; Tokushuku, K.; Tolley, E.; Tomlinson, L.; Tomoto, M.; Tompkins, L.; Toms, K.; Tong, B.; Torrence, E.; Torres, H.; Torróâ Pastor, E.; Toth, J.; Touchard, F.; Tovey, D. R.; Trefzger, T.; Tricoli, A.; Trigger, I. M.; Trincaz-Duvoid, S.; Tripiana, M. F.; Trischuk, W.; Trocmé, B.; Trofymov, A.; Troncon, C.; Trottier-McDonald, M.; Trovatelli, M.; Truong, L.; Trzebinski, M.; Trzupek, A.; Tseng, J. C.-L.; Tsiareshka, P. V.; Tsipolitis, G.; Tsirintanis, N.; Tsiskaridze, S.; Tsiskaridze, V.; Tskhadadze, E. G.; Tsui, K. M.; Tsukerman, I. I.; Tsulaia, V.; Tsuno, S.; Tsybychev, D.; Tu, Y.; Tudorache, A.; Tudorache, V.; Tuna, A. N.; Tupputi, S. A.; Turchikhin, S.; Turecek, D.; Turgeman, D.; Turra, R.; Turvey, A. J.; Tuts, P. M.; Tyndel, M.; Ucchielli, G.; Ueda, I.; Ughetto, M.; Ukegawa, F.; Unal, G.; Undrus, A.; Unel, G.; Ungaro, F. C.; Unno, Y.; Unverdorben, C.; Urban, J.; Urquijo, P.; Urrejola, P.; Usai, G.; Vacavant, L.; Vacek, V.; Vachon, B.; Valderanis, C.; Valdesâ Santurio, E.; Valencic, N.; Valentinetti, S.; Valero, A.; Valéry, L.; Valkar, S.; Vallsâ Ferrer, J. A.; Vanâ Denâ Wollenberg, W.; Vanâ Derâ Deijl, P. C.; Vanâ Derâ Graaf, H.; Vanâ Eldik, N.; Vanâ Gemmeren, P.; Vanâ Nieuwkoop, J.; Vanâ Vulpen, I.; Vanâ Woerden, M. C.; Vanadia, M.; Vandelli, W.; Vanguri, R.; Vaniachine, A.; Vankov, P.; Vardanyan, G.; Vari, R.; Varnes, E. W.; Varol, T.; Varouchas, D.; Vartapetian, A.; Varvell, K. E.; Vasquez, J. G.; Vasquez, G. A.; Vazeille, F.; Vazquezâ Schroeder, T.; Veatch, J.; Veeraraghavan, V.; Veloce, L. M.; Veloso, F.; Veneziano, S.; Ventura, A.; Venturi, M.; Venturi, N.; Venturini, A.; Vercesi, V.; Verducci, M.; Verkerke, W.; Vermeulen, J. C.; Vest, A.; Vetterli, M. C.; Viazlo, O.; Vichou, I.; Vickey, T.; Vickeyâ Boeriu, O. E.; Viehhauser, G. H. A.; Viel, S.; Vigani, L.; Villa, M.; Villaplanaâ Perez, M.; Vilucchi, E.; Vincter, M. G.; Vinogradov, V. B.; Vittori, C.; Vivarelli, I.; Vlachos, S.; Vlasak, M.; Vogel, M.; Vokac, P.; Volpi, G.; Volpi, M.; Vonâ Derâ Schmitt, H.; Vonâ Toerne, E.; Vorobel, V.; Vorobev, K.; Vos, M.; Voss, R.; Vossebeld, J. H.; Vranjes, N.; Vranjesâ Milosavljevic, M.; Vrba, V.; Vreeswijk, M.; Vuillermet, R.; Vukotic, I.; Vykydal, Z.; Wagner, P.; Wagner, W.; Wahlberg, H.; Wahrmund, S.; Wakabayashi, J.; Walder, J.; Walker, R.; Walkowiak, W.; Wallangen, V.; Wang, C.; Wang, C.; Wang, F.; Wang, H.; Wang, H.; Wang, J.; Wang, J.; Wang, K.; Wang, R.; Wang, S. M.; Wang, T.; Wang, T.; Wang, W.; Wang, X.; Wanotayaroj, C.; Warburton, A.; Ward, C. P.; Wardrope, D. R.; Washbrook, A.; Watkins, P. M.; Watson, A. T.; Watson, M. F.; Watts, G.; Watts, S.; Waugh, B. M.; Webb, S.; Weber, M. S.; Weber, S. W.; Webster, J. S.; Weidberg, A. R.; Weinert, B.; Weingarten, J.; Weiser, C.; Weits, H.; Wells, P. S.; Wenaus, T.; Wengler, T.; Wenig, S.; Wermes, N.; Werner, M.; Werner, M. D.; Werner, P.; Wessels, M.; Wetter, J.; Whalen, K.; Whallon, N. L.; Wharton, A. M.; White, A.; White, M. J.; White, R.; Whiteson, D.; Wickens, F. J.; Wiedenmann, W.; Wielers, M.; Wiglesworth, C.; Wiik-Fuchs, L. A. M.; Wildauer, A.; Wilk, F.; Wilkens, H. G.; Williams, H. H.; Williams, S.; Willis, C.; Willocq, S.; Wilson, J. A.; Wingerter-Seez, I.; Winklmeier, F.; Winston, O. J.; Winter, B. T.; Wittgen, M.; Wittkowski, J.; Wolf, T. M. H.; Wolter, M. W.; Wolters, H.; Worm, S. D.; Wosiek, B. K.; Wotschack, J.; Woudstra, M. J.; Wozniak, K. W.; Wu, M.; Wu, M.; Wu, S. L.; Wu, X.; Wu, Y.; Wyatt, T. R.; Wynne, B. M.; Xella, S.; Xu, D.; Xu, L.; Yabsley, B.; Yacoob, S.; Yamaguchi, D.; Yamaguchi, Y.; Yamamoto, A.; Yamamoto, S.; Yamanaka, T.; Yamauchi, K.; Yamazaki, Y.; Yan, Z.; Yang, H.; Yang, H.; Yang, Y.; Yang, Z.; Yao, W.-M.; Yap, Y. C.; Yasu, Y.; Yatsenko, E.; Yauâ Wong, K. H.; Ye, J.; Ye, S.; Yeletskikh, I.; Yen, A. L.; Yildirim, E.; Yorita, K.; Yoshida, R.; Yoshihara, K.; Young, C.; Young, C. J. S.; Youssef, S.; Yu, D. R.; Yu, J.; Yu, J. M.; Yu, J.; Yuan, L.; Yuen, S. P. Y.; Yusuff, I.; Zabinski, B.; Zaidan, R.; Zaitsev, A. M.; Zakharchuk, N.; Zalieckas, J.; Zaman, A.; Zambito, S.; Zanello, L.; Zanzi, D.; Zeitnitz, C.; Zeman, M.; Zemla, A.; Zeng, J. C.; Zeng, Q.; Zengel, K.; Zenin, O.; Ženiš, T.; Zerwas, D.; Zhang, D.; Zhang, F.; Zhang, G.; Zhang, H.; Zhang, J.; Zhang, L.; Zhang, R.; Zhang, R.; Zhang, X.; Zhang, Z.; Zhao, X.; Zhao, Y.; Zhao, Z.; Zhemchugov, A.; Zhong, J.; Zhou, B.; Zhou, C.; Zhou, L.; Zhou, L.; Zhou, M.; Zhou, N.; Zhu, C. G.; Zhu, H.; Zhu, J.; Zhu, Y.; Zhuang, X.; Zhukov, K.; Zibell, A.; Zieminska, D.; Zimine, N. I.; Zimmermann, C.; Zimmermann, S.; Zinonos, Z.; Zinser, M.; Ziolkowski, M.; Živković, L.; Zobernig, G.; Zoccoli, A.; Zurâ Nedden, M.; Zwalinski, L.; Atlas Collaboration

2017-12-01

Bose-Einstein correlations between identified charged pions are measured for p +Pb collisions at √{sNN}=5.02 TeV using data recorded by the ATLAS detector at the CERN Large Hadron Collider corresponding to a total integrated luminosity of 28 nb-1 . Pions are identified using ionization energy loss measured in the pixel detector. Two-particle correlation functions and the extracted source radii are presented as a function of collision centrality as well as the average transverse momentum (kT) and rapidity (yππ ★) of the pair. Pairs are selected with a rapidity -2

Effect of base sequence on the DNA cross-linking properties of pyrrolobenzodiazepine (PBD) dimers

PubMed Central

Rahman, Khondaker M.; James, Colin H.; Thurston, David E.

2011-01-01

Pyrrolo[2,1-c][1,4]benzodiazepine (PBD) dimers are synthetic sequence-selective DNA minor-groove cross-linking agents that possess two electrophilic imine moieties (or their equivalent) capable of forming covalent aminal linkages with guanine C2-NH2 functionalities. The PBD dimer SJG-136, which has a C8–O–(CH2)3–O–C8′′ central linker joining the two PBD moieties, is currently undergoing phase II clinical trials and current research is focused on developing analogues of SJG-136 with different linker lengths and substitution patterns. Using a reversed-phase ion pair HPLC/MS method to evaluate interaction with oligonucleotides of varying length and sequence, we recently reported (JACS, 2009, 131, 13 756) that SJG-136 can form three different types of adducts: inter- and intrastrand cross-linked adducts, and mono-alkylated adducts. These studies have now been extended to include PBD dimers with a longer central linker (C8–O–(CH2)5–O–C8′), demonstrating that the type and distribution of adducts appear to depend on (i) the length of the C8/C8′-linker connecting the two PBD units, (ii) the positioning of the two reactive guanine bases on the same or opposite strands, and (iii) their separation (i.e. the number of base pairs, usually ATs, between them). Based on these data, a set of rules are emerging that can be used to predict the DNA–interaction behaviour of a PBD dimer of particular C8–C8′ linker length towards a given DNA sequence. These observations suggest that it may be possible to design PBD dimers to target specific DNA sequences. PMID:21427082

Spatial variation of dosimetric leaf gap and its impact on dose delivery

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

Kumaraswamy, Lalith K., E-mail: Lalith.Kumaraswamy@roswellpark.org; Schmitt, Jonathan D.; Bailey, Daniel W.

Purpose: During dose calculation, the Eclipse treatment planning system (TPS) retracts the multileaf collimator (MLC) leaf positions by half of the dosimetric leaf gap (DLG) value (measured at central axis) for all leaf positions in a dynamic MLC plan to accurately model the rounded leaf ends. The aim of this study is to map the variation of DLG along the travel path of each MLC leaf pair and quantify how this variation impacts delivered dose. Methods: 6 MV DLG values were measured for all MLC leaf pairs in increments of 1.0 cm (from the line intersecting the CAX and perpendicularmore » to MLC motion) to 13.0 cm off axis distance at dmax. The measurements were performed on two Varian linear accelerators, both employing the Millennium 120-leaf MLCs. The measurements were performed at several locations in the beam with both a Sun Nuclear MapCHECK device and a PTW pinpoint ion chamber. Results: The measured DLGs for the middle 40 MLC leaf pairs (each 0.5 cm width) at positions along a line through the CAX and perpendicular to MLC leaf travel direction were very similar, varying maximally by only 0.2 mm. The outer 20 MLC leaf pairs (each 1.0 cm width) have much lower DLG values, about 0.3–0.5 mm lower than the central MLC leaf pair, at their respective central line position. Overall, the mean and the maximum variation between the 0.5 cm width leaves and the 1.0 cm width leaf pairs are 0.32 and 0.65 mm, respectively. Conclusions: The spatial variation in DLG is caused by the variation of intraleaf transmission through MLC leaves. Fluences centered on the CAX would not be affected since DLG does not vary; but any fluences residing significantly off axis with narrow sweeping leaves may exhibit significant dose differences. This is due to the fact that there are differences in DLG between the true DLG exhibited by the 1.0 cm width outer leaves and the constant DLG value utilized by the TPS for dose calculation. Since there are large differences in DLG between the 0.5 cm width leaf pairs and 1.0 cm width leaf pairs, there is a need to correct the TPS plans, especially those with high modulation (narrow dynamic MLC gap), with 2D variation of DLG.« less

Turbine nozzle attachment system

DOEpatents

Norton, Paul F.; Shaffer, James E.

1995-01-01

A nozzle guide vane assembly having a preestablished rate of thermal expansion is positioned in a gas turbine engine and being attached to conventional metallic components. The nozzle guide vane assembly includes a pair of legs extending radially outwardly from an outer shroud and a pair of mounting legs extending radially inwardly from an inner shroud. Each of the pair of legs and mounting legs have a pair of holes therein. A plurality of members attached to the gas turbine engine have a plurality of bores therein which axially align with corresponding ones of the pair of holes in the legs. A plurality of pins are positioned within the corresponding holes and bores radially positioning the nozzle guide vane assembly about a central axis of the gas turbine engine.

Turbine nozzle attachment system

DOEpatents

Norton, P.F.; Shaffer, J.E.

1995-10-24

A nozzle guide vane assembly having a preestablished rate of thermal expansion is positioned in a gas turbine engine and is attached to conventional metallic components. The nozzle guide vane assembly includes a pair of legs extending radially outwardly from an outer shroud and a pair of mounting legs extending radially inwardly from an inner shroud. Each of the pair of legs and mounting legs have a pair of holes therein. A plurality of members attached to the gas turbine engine have a plurality of bores therein which axially align with corresponding ones of the pair of holes in the legs. A plurality of pins are positioned within the corresponding holes and bores radially positioning the nozzle guide vane assembly about a central axis of the gas turbine engine. 3 figs.

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

NASA Astrophysics Data System (ADS)

Kharin, Nikolay A.

2001-05-01

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

Developing Single-Molecule TPM Experiments for Direct Observation of Successful RecA-Mediated Strand Exchange Reaction

PubMed Central

Fan, Hsiu-Fang; Cox, Michael M.; Li, Hung-Wen

2011-01-01

RecA recombinases play a central role in homologous recombination. Once assembled on single-stranded (ss) DNA, RecA nucleoprotein filaments mediate the pairing of homologous DNA sequences and strand exchange processes. We have designed two experiments based on tethered particle motion (TPM) to investigate the fates of the invading and the outgoing strands during E. coli RecA-mediated pairing and strand exchange at the single-molecule level in the absence of force. TPM experiments measure the tethered bead Brownian motion indicative of the DNA tether length change resulting from RecA binding and dissociation. Experiments with beads labeled on either the invading strand or the outgoing strand showed that DNA pairing and strand exchange occurs successfully in the presence of either ATP or its non-hydrolyzable analog, ATPγS. The strand exchange rates and efficiencies are similar under both ATP and ATPγS conditions. In addition, the Brownian motion time-courses suggest that the strand exchange process progresses uni-directionally in the 5′-to-3′ fashion, using a synapse segment with a wide and continuous size distribution. PMID:21765895

An Ultra-Sensitive Electrometer based on the Cavity-Embedded Cooper-Pair Transistor

NASA Astrophysics Data System (ADS)

Li, Juliang; Miller, Marco; Rimberg, Alex

2015-03-01

We discuss use of a cavity-embedded Cooper-pair transistor (cCPT) as a potentially quantum-limited electrometer. The cCPT consists of a Cooper pair transistor placed at the voltage antinode of a 5.7 GHz shorted quarter-wave resonator so that the CPT provides a galvanic connection between the cavity's central conductor and ground plane. The quantum inductance of the CPT, which appears in parallel with the effective inductance of the cavity resonance, can be modulated by application of either a gate voltage to the CPT island or a flux bias to the CPT/cavity loop. Changes in the CPT inductance shift the cavity resonant frequency, and therefore the phase of a microwave signal reflected from the cavity. The reflected wave is amplified by both SLUG and HEMT amplifiers before its phase is measured. Results of recent measurements on the cCPT electrometer will be compared with theoretical predictions. This work was supported by the NSF under Grant No. DMR-1104821, by the ARO under Contract No, W911NF-13-1-0377 and by AFOSR/DARPA under Agreement No. FA8750-12-2-0339.

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

NASA Astrophysics Data System (ADS)

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

2004-08-01

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

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

NASA Astrophysics Data System (ADS)

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

2004-08-01

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

[Electroencephalographic characteristic of cognitive-specific alerting attention in verbal learning--III: Localized characteristics of EEG spatial synchronization].

PubMed

Dan'ko, S G; Kachalova, L M; Solov'eva, M L

2010-01-01

Electroencephalograms (EEG) were recorder in 19 standard derivations in 88 healthy subjects, while they were in the states: rest with eyes open; memorization (learning) of verbal bilingual semantic pairs (Latin and Russian languages); the retrieval of the rote information from memory (control). We compared estimates of EEG coherence in these states for the frequency bands theta (4-7 Hz), alpha-1 (7-10 Hz), alpha-2 (10-13 Hz), beta-1 (13-18 Hz), beta-2 (18-30 Hz), gamma (30-40 Hz). When compared with the rest most strongly expressed: for memorization a decrease of coherence in the pairs of derivations from frontal and central areas of the cortex in the EEG frequency bands; for retrieval an increase of coherence in interhemispheric derivation pairs of pariental-occipital region in majority of the frequency bands. For the retrieval also increases of coherence in the beta2 and gamma bands, along with coherence decreases at low frequencies take place in pairs formed by derivations from the parieto-occipital region with derivations from the frontal and the central ones. Dynamics of EEG coherence in comparisons of memorization and retrieval from the rest and each are expressed significantly more in the interhemispheric and crosshemispheric pairs of derivations than in the intrahemispheric pairs. Revealed topographic specificity of the dynamics of EEG coherence by changing the states is considered in terms of ideas about cognitive-specific forms of sustained goal-directed mental attention.

Sordaria, a model system to uncover links between meiotic pairing and recombination.

PubMed

Zickler, Denise; Espagne, Eric

2016-06-01

The mycelial fungus Sordaria macrospora was first used as experimental system for meiotic recombination. This review shows that it provides also a powerful cytological system for dissecting chromosome dynamics in wild-type and mutant meioses. Fundamental cytogenetic findings include: (1) the identification of presynaptic alignment as a key step in pairing of homologous chromosomes. (2) The discovery that biochemical complexes that mediate recombination at the DNA level concomitantly mediate pairing of homologs. (3) This pairing process involves not only resolution but also avoidance of chromosomal entanglements and the resolution system includes dissolution of constraining DNA recombination interactions, achieved by a unique role of Mlh1. (4) Discovery that the central components of the synaptonemal complex directly mediate the re-localization of the recombination proteins from on-axis to in-between homologue axis positions. (5) Identification of putative STUbL protein Hei10 as a structure-based signal transduction molecule that coordinates progression and differentiation of recombinational interactions at multiple stages. (6) Discovery that a single interference process mediates both nucleation of the SC and designation of crossover sites, thereby ensuring even spacing of both features. (7) Discovery of local modulation of sister-chromatid cohesion at sites of crossover recombination. Copyright © 2016 Elsevier Ltd. All rights reserved.

Plate tectonics and biogeographical patterns of the Pseudophoxinus (Pisces: Cypriniformes) species complex of central Anatolia, Turkey.

PubMed

Hrbek, Tomas; Stölting, Kai N; Bardakci, Fevzi; Küçük, Fahrettin; Wildekamp, Rudolf H; Meyer, Axel

2004-07-01

We investigated the phylogenetic relationships of Pseudophoxinus (Cyprinidae: Leuciscinae) species from central Anatolia, Turkey to test the hypothesis of geographic speciation driven by early Pliocene orogenic events. We analyzed 1141 aligned base pairs of the complete cytochrome b mitochondrial gene. Phylogenetic relationships reconstructed by maximum likelihood, Bayesian likelihood, and maximum parsimony methods are identical, and generally well supported. Species and clades are restricted to geologically well-defined units, and are deeply divergent from each other. The basal diversification of central Anatolian Pseudophoxinus is estimated to have occurred approximately 15 million years ago. Our results are in agreement with a previous study of the Anatolian fish genus Aphanius that also shows a diversification pattern driven by the Pliocene orogenic events. The distribution of clades of Aphanius and Pseudophoxinus overlap, and areas of distribution comprise the same geological units. The geological history of Anatolia is likely to have had a major impact on the diversification history of many taxa occupying central Anatolia; many of these taxa are likely to be still unrecognized as distinct. Copyright 2004 Elsevier Inc.

A broadband Soleil-Babinet compensator for ultrashort light pulses

NASA Astrophysics Data System (ADS)

Xu, Shixiang; Ma, Yingkun; Cai, Yi; Lu, Xiaowei; Zeng, Xuanke; Chen, Hongyi; Li, Jingzhen

2013-12-01

This letter reports a novel design for a broadband Soleil-Babinet compensator including two pairs of optical wedges plus one plate. According to our birefringent dispersion compensation model, we can eliminate the first-order birefringent phase retardation (BPR) dispersion by using three different birefringent crystals. Our results show a Soleil-Babinet compensator based on a MgF2/ADP/KDP combination can work from 0° to 360° phase compensation with the maximal residual BPR less than 6° within the spectral region from 0.65 to 0.95 μm. The residual BPR of the compensator increases monotonically with the spectral deviation from the designed central wavelength, so our compensator is very suitable to be used for broadband laser pulses with most of their energies around the central wavelengths.

Genetic differentiation in blue shark, Prionace glauca, from the central Pacific Ocean, as inferred by mitochondrial cytochrome b region.

PubMed

Li, Weiwen; Dai, Xiaojie; Zhu, Jiangfeng; Tian, Siquan; He, Shan; Wu, Feng

2017-07-01

Six hundred and ninety-seven base pairs of cytochrome b gene of mtDNA was sequenced and analyzed for 78 blue shark Prionace glauca individuals from three sampled locations in the central Pacific Ocean (CPO). In total, three polymorphic sites were detected which defined four haplotypes. The haplotype diversity (h) ranged from 0.517 to 0.768, and nucleotide diversity (π) was between 0.0007 and 0.0011. Analysis of molecular variance indicated a non-significant differentiation among subpopulations. Furthermore, pairwise F ST score analysis revealed a non-significant differentiation among three sampled regions. Generally, low genetic differences were found between different geographic locations in the CPO. This study suggests a single panmictic population of P. glauca in the CPO.

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

NASA Astrophysics Data System (ADS)

Zhao, P.; Peng, Z.

2008-12-01

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

Clustering of cycloidal wave energy converters

DOEpatents

Siegel, Stefan G.

2016-03-29

A wave energy conversion system uses a pair of wave energy converters (WECs) on respective active mountings on a floating platform, so that the separation of the WECs from each other or from a central WEC can be actively adjusted according to the wavelength of incident waves. The adjustable separation facilitates operation of the system to cancel reactive forces, which may be generated during wave energy conversion. Modules on which such pairs of WECs are mounted can be assembled with one or more central WECs to form large clusters in which reactive forces and torques can be made to cancel. WECs of different sizes can be employed to facilitate cancelation of reactive forces and torques.

Coverage centralities for temporal networks*

NASA Astrophysics Data System (ADS)

Takaguchi, Taro; Yano, Yosuke; Yoshida, Yuichi

2016-02-01

Structure of real networked systems, such as social relationship, can be modeled as temporal networks in which each edge appears only at the prescribed time. Understanding the structure of temporal networks requires quantifying the importance of a temporal vertex, which is a pair of vertex index and time. In this paper, we define two centrality measures of a temporal vertex based on the fastest temporal paths which use the temporal vertex. The definition is free from parameters and robust against the change in time scale on which we focus. In addition, we can efficiently compute these centrality values for all temporal vertices. Using the two centrality measures, we reveal that distributions of these centrality values of real-world temporal networks are heterogeneous. For various datasets, we also demonstrate that a majority of the highly central temporal vertices are located within a narrow time window around a particular time. In other words, there is a bottleneck time at which most information sent in the temporal network passes through a small number of temporal vertices, which suggests an important role of these temporal vertices in spreading phenomena. Contribution to the Topical Issue "Temporal Network Theory and Applications", edited by Petter Holme.Supplementary material in the form of one pdf file available from the Journal web page at http://dx.doi.org/10.1140/epjb/e2016-60498-7

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

PubMed

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

2014-01-01

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

A short walk in quantum probability.

PubMed

Hudson, Robin

2018-04-28

This is a personal survey of aspects of quantum probability related to the Heisenberg commutation relation for canonical pairs. Using the failure, in general, of non-negativity of the Wigner distribution for canonical pairs to motivate a more satisfactory quantum notion of joint distribution, we visit a central limit theorem for such pairs and a resulting family of quantum planar Brownian motions which deform the classical planar Brownian motion, together with a corresponding family of quantum stochastic areas.This article is part of the themed issue 'Hilbert's sixth problem'. © 2018 The Author(s).

The Influence of Landscape Heterogeneity - Ground Beetles (Coleoptera: Carabidae) in Fthiotida, Central Greece

PubMed Central

2014-01-01

Abstract Pitfall traps were used to sample Carabidae in agricultural land of the Spercheios valley, Fthiotida, Central Greece. Four pairs of cultivated fields were sampled. One field of each pair was located in a heterogeneous area and the other in a more homogeneous area. Heterogeneous areas were composed of small fields. They had high percentages of non-cropped habitats and a high diversity of land use types. Homogeneous areas were composed of larger fields. They had lower percentages of non-cropped habitats and a lower diversity of land use types. One pair of fields had been planted with cotton, one with maize, one with olives and one with wheat. Altogether 28 carabid species were recorded. This paper describes the study areas, the sampling methods used and presents the data collected during the study. Neither heterogeneous nor homogeneous areas had consistently higher abundance levels, activity density levels, species richness levels or diversity levels. However, significant differences were seen in some of the comparisons between heterogeneous and homogeneous areas. PMID:24891833

Search for quark compositeness with the dijet centrality ratio in pp collisions at √s=7 TeV.

PubMed

Khachatryan, V; Sirunyan, A M; Tumasyan, A; Adam, W; Bergauer, T; Dragicevic, M; Erö, J; Fabjan, C; Friedl, M; Frühwirth, R; Ghete, V M; Hammer, J; Hänsel, S; Hartl, C; Hoch, M; Hörmann, N; Hrubec, J; Jeitler, M; Kasieczka, G; Kiesenhofer, W; Krammer, M; Liko, D; Mikulec, I; Pernicka, M; Rohringer, H; Schöfbeck, R; Strauss, J; Taurok, A; Teischinger, F; Waltenberger, W; Walzel, G; Widl, E; Wulz, C-E; Mossolov, V; Shumeiko, N; Gonzalez, J Suarez; Benucci, L; Ceard, L; De Wolf, E A; Janssen, X; Maes, T; Mucibello, L; Ochesanu, S; Roland, B; Rougny, R; Selvaggi, M; Van Haevermaet, H; Van Mechelen, P; Van Remortel, N; Adler, V; Beauceron, S; Blyweert, S; D'Hondt, J; Devroede, O; Kalogeropoulos, A; Maes, J; Maes, M; Tavernier, S; Van Doninck, W; Van Mulders, P; Van Onsem, G P; Villella, I; Charaf, O; Clerbaux, B; De Lentdecker, G; Dero, V; Gay, A P R; Hammad, G H; Hreus, T; Marage, P E; Thomas, L; Vander Velde, C; Vanlaer, P; Wickens, J; Costantini, S; Grunewald, M; Klein, B; Marinov, A; Ryckbosch, D; Thyssen, F; Tytgat, M; Vanelderen, L; Verwilligen, P; Walsh, S; Zaganidis, N; Basegmez, S; Bruno, G; Caudron, J; De Favereau De Jeneret, J; Delaere, C; Demin, P; Favart, D; Giammanco, A; Grégoire, G; Hollar, J; Lemaitre, V; Militaru, O; Ovyn, S; Pagano, D; Pin, A; Piotrzkowski, K; Quertenmont, L; Schul, N; Beliy, N; Caebergs, T; Daubie, E; Alves, G A; De JesusDamiao, D; Pol, M E; Souza, M H G; Carvalho, W; Da Costa, E M; Martins, C De Oliveira; De Souza, S Fonseca; Mundim, L; Nogima, H; Oguri, V; Goicochea, J M Otalora; Da Silva, W L Prado; Santoro, A; Do Amaral, S M Silva; Sznajder, A; De Araujo, F Torres Da Silva; Dias, F A; Dias, M A F; Tomei, T R Fernandez Perez; Gregores, E M; Marinho, F; Novaes, S F; Padula, Sandra S; Darmenov, N; Dimitrov, L; Genchev, V; Iaydjiev, P; Piperov, S; Rodozov, M; Stoykova, S; Sultanov, G; Tcholakov, V; Trayanov, R; Vankov, I; Dyulendarova, M; Hadjiiska, R; Kozhuharov, V; Litov, L; Marinova, E; Mateev, M; Pavlov, B; Petkov, P; Bian, J G; Chen, G M; Chen, H S; Jiang, C H; Liang, D; Liang, S; Wang, J; Wang, J; Wang, X; Wang, Z; Yang, M; Zang, J; Zhang, Z; Ban, Y; Guo, S; Hu, Z; Li, W; Mao, Y; Qian, S J; Teng, H; Zhu, B; Cabrera, A; Moreno, B Gomez; Rios, A A Ocampo; Oliveros, A F Osorio; Sanabria, J C; Godinovic, N; Lelas, D; Lelas, K; Plestina, R; Polic, D; Puljak, I; Antunovic, Z; Dzelalija, M; Brigljevic, V; Duric, S; Kadija, K; Morovic, S; Attikis, A; Fereos, R; Galanti, M; Mousa, J; Nicolaou, C; Ptochos, F; Razis, P A; Rykaczewski, H; Abdel-basit, A; Assran, Y; Mahmoud, M A; Hektor, A; Kadastik, M; Kannike, K; Müntel, M; Raidal, M; Rebane, L; Azzolini, V; Eerola, P; Czellar, S; Härkönen, J; Heikkinen, A; Karimäki, V; Kinnunen, R; Klem, J; Kortelainen, M J; Lampén, T; Lassila-Perini, K; Lehti, S; Lindén, T; Luukka, P; Mäenpää, T; Tuominen, E; Tuominiemi, J; Tuovinen, E; Ungaro, D; Wendland, L; Banzuzi, K; Korpela, A; Tuuva, T; Sillou, D; Besancon, M; Dejardin, M; Denegri, D; Fabbro, B; Faure, J L; Ferri, F; Ganjour, S; Gentit, F X; Givernaud, A; Gras, P; de Monchenault, G Hamel; Jarry, P; Locci, E; Malcles, J; Marionneau, M; Millischer, L; Rander, J; Rosowsky, A; Titov, M; Verrecchia, P; Baffioni, S; Bianchini, L; Bluj, M; Broutin, C; Busson, P; Charlot, C; Dobrzynski, L; de Cassagnac, R Granier; Haguenauer, M; Miné, P; Mironov, C; Ochando, C; Paganini, P; Sabes, D; Salerno, R; Sirois, Y; Thiebaux, C; Wyslouch, B; Zabi, A; Agram, J-L; Andrea, J; Besson, A; Bloch, D; Bodin, D; Brom, J-M; Cardaci, M; Chabert, E C; Collard, C; Conte, E; Drouhin, F; Ferro, C; Fontaine, J-C; Gelé, D; Goerlach, U; Greder, S; Juillot, P; Karim, M; Le Bihan, A-C; Mikami, Y; Van Hove, P; Fassi, F; Mercier, D; Baty, C; Beaupere, N; Bedjidian, M; Bondu, O; Boudoul, G; Boumediene, D; Brun, H; Chanon, N; Chierici, R; Contardo, D; Depasse, P; El Mamouni, H; Falkiewicz, A; Fay, J; Gascon, S; Ille, B; Kurca, T; Le Grand, T; Lethuillier, M; Mirabito, L; Perries, S; Sordini, V; Tosi, S; Tschudi, Y; Verdier, P; Xiao, H; Roinishvili, V; Anagnostou, G; Edelhoff, M; Feld, L; Heracleous, N; Hindrichs, O; Jussen, R; Klein, K; Merz, J; Mohr, N; Ostapchuk, A; Perieanu, A; Raupach, F; Sammet, J; Schael, S; Sprenger, D; Weber, H; Weber, M; Wittmer, B; Ata, M; Bender, W; Erdmann, M; Frangenheim, J; Hebbeker, T; Hinzmann, A; Hoepfner, K; Hof, C; Klimkovich, T; Klingebiel, D; Kreuzer, P; Lanske, D; Magass, C; Masetti, G; Merschmeyer, M; Meyer, A; Papacz, P; Pieta, H; Reithler, H; Schmitz, S A; Sonnenschein, L; Steggemann, J; Teyssier, D; Bontenackels, M; Davids, M; Duda, M; Flügge, G; Geenen, H; Giffels, M; Ahmad, W Haj; Heydhausen, D; Kress, T; Kuessel, Y; Linn, A; Nowack, A; Perchalla, L; Pooth, O; Rennefeld, J; Sauerland, P; Stahl, A; Thomas, M; Tornier, D; Zoeller, M H; Martin, M Aldaya; Behrenhoff, W; Behrens, U; Bergholz, M; Borras, K; Cakir, A; Campbell, A; Castro, E; Dammann, D; Eckerlin, G; Eckstein, D; Flossdorf, A; Flucke, G; Geiser, A; Glushkov, I; Hauk, J; Jung, H; Kasemann, M; Katkov, I; Katsas, P; Kleinwort, C; Kluge, H; Knutsson, A; Krücker, D; Kuznetsova, E; Lange, W; Lohmann, W; Mankel, R; Marienfeld, M; Melzer-Pellmann, I-A; Meyer, A B; Mnich, J; Mussgiller, A; Olzem, J; Parenti, A; Raspereza, A; Raval, A; Schmidt, R; Schoerner-Sadenius, T; Sen, N; Stein, M; Tomaszewska, J; Volyanskyy, D; Walsh, R; Wissing, C; Autermann, C; Bobrovskyi, S; Draeger, J; Enderle, H; Gebbert, U; Kaschube, K; Kaussen, G; Klanner, R; Mura, B; Naumann-Emme, S; Nowak, F; Pietsch, N; Sander, C; Schettler, H; Schleper, P; Schröder, M; Schum, T; Schwandt, J; Srivastava, A K; Stadie, H; Steinbrück, G; Thomsen, J; Wolf, R; Bauer, J; Buege, V; Chwalek, T; Daeuwel, D; De Boer, W; Dierlamm, A; Dirkes, G; Feindt, M; Gruschke, J; Hackstein, C; Hartmann, F; Heinrich, M; Held, H; Hoffmann, K H; Honc, S; Kuhr, T; Martschei, D; Mueller, S; Müller, Th; Neuland, M B; Niegel, M; Oberst, O; Oehler, A; Ott, J; Peiffer, T; Piparo, D; Quast, G; Rabbertz, K; Ratnikov, F; Renz, M; Sabellek, A; Saout, C; Scheurer, A; Schieferdecker, P; Schilling, F-P; Schott, G; Simonis, H J; 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Kypreos, T; Matchev, K; Mitselmakher, G; Muniz, L; Pakhotin, Y; Petterson, M; Prescott, C; Remington, R; Schmitt, M; Scurlock, B; Sellers, P; Skhirtladze, N; Snowball, M; Wang, D; Yelton, J; Zakaria, M; Ceron, C; Gaultney, V; Kramer, L; Lebolo, L M; Linn, S; Markowitz, P; Martinez, G; Mesa, D; Rodriguez, J L; Adams, T; Askew, A; Bochenek, J; Chen, J; Diamond, B; Gleyzer, S V; Haas, J; Hagopian, S; Hagopian, V; Jenkins, M; Johnson, K F; Prosper, H; Sekmen, S; Veeraraghavan, V; Baarmand, M M; Dorney, B; Guragain, S; Hohlmann, M; Kalakhety, H; Ralich, R; Vodopiyanov, I; Adams, M R; Anghel, I M; Apanasevich, L; Bai, Y; Bazterra, V E; Betts, R R; Callner, J; Cavanaugh, R; Dragoiu, C; Garcia-Solis, E J; Gerber, C E; Hofman, D J; Khalatyan, S; Lacroix, F; O'Brien, C; Silvestre, C; Smoron, A; Strom, D; Varelas, N; Akgun, U; Albayrak, E A; Bilki, B; Cankocak, K; Clarida, W; Duru, F; Lae, C K; McCliment, E; Merlo, J-P; Mermerkaya, H; Mestvirishvili, A; Moeller, A; Nachtman, J; Newsom, C R; Norbeck, E; Olson, J; Onel, Y; Ozok, F; Sen, S; Wetzel, J; Yetkin, T; Yi, K; Barnett, B A; Blumenfeld, B; Bonato, A; Eskew, C; Fehling, D; Giurgiu, G; Gritsan, A V; Guo, Z J; Hu, G; Maksimovic, P; Rappoccio, S; Swartz, M; Tran, N V; Whitbeck, A; Baringer, P; Bean, A; Benelli, G; Grachov, O; Murray, M; Noonan, D; Radicci, V; Sanders, S; Wood, J S; Zhukova, V; Bandurin, D; Bolton, T; Chakaberia, I; Ivanov, A; Makouski, M; Maravin, Y; Shrestha, S; Svintradze, I; Wan, Z; Gronberg, J; Lange, D; Wright, D; Baden, A; Boutemeur, M; Eno, S C; Ferencek, D; Gomez, J A; Hadley, N J; Kellogg, R G; Kirn, M; Lu, Y; Mignerey, A C; Rossato, K; Rumerio, P; Santanastasio, F; Skuja, A; Temple, J; Tonjes, M B; Tonwar, S C; Twedt, E; Alver, B; Bauer, G; Bendavid, J; Busza, W; Butz, E; Cali, I A; Chan, M; Dutta, V; Everaerts, P; Ceballos, G Gomez; Goncharov, M; Hahn, K A; Harris, P; Kim, Y; Klute, M; Lee, Y-J; Li, W; Loizides, C; Lopez, J; Luckey, P D; Ma, T; Nahn, S; Paus, C; Roland, C; Roland, G; Rudolph, M; Stephans, G S F; Sumorok, K; Sung, K; Wenger, E A; Xie, S; Yang, M; Yilmaz, Y; Yoon, A S; Zanetti, M; Cole, P; Cooper, S I; Cushman, P; Dahmes, B; De Benedetti, A; Dudero, P R; Franzoni, G; Haupt, J; Klapoetke, K; Kubota, Y; Mans, J; Rekovic, V; Rusack, R; Sasseville, M; Singovsky, A; Cremaldi, L M; Godang, R; Kroeger, R; Perera, L; Rahmat, R; Sanders, D A; Summers, D; Bloom, K; Bose, S; Butt, J; Claes, D R; Dominguez, A; Eads, M; Keller, J; Kelly, T; Kravchenko, I; Lazo-Flores, J; Lundstedt, C; Malbouisson, H; Malik, S; Snow, G R; Baur, U; Godshalk, A; Iashvili, I; Kharchilava, A; Kumar, A; Smith, K; Zennamo, J; Alverson, G; Barberis, E; Baumgartel, D; Boeriu, O; Chasco, M; Kaadze, K; Reucroft, S; Swain, J; Wood, D; Zhang, J; Anastassov, A; Kubik, A; Odell, N; Ofierzynski, R A; Pollack, B; Pozdnyakov, A; Schmitt, M; Stoynev, S; Velasco, M; Won, S; Antonelli, L; Berry, D; Hildreth, M; Jessop, C; Karmgard, D J; Kolb, J; Kolberg, T; Lannon, K; Luo, W; Lynch, S; Marinelli, N; Morse, D M; Pearson, T; Ruchti, R; Slaunwhite, J; Valls, N; Warchol, J; Wayne, M; Ziegler, J; Bylsma, B; Durkin, L S; Gu, J; Hill, C; Killewald, P; Ling, T Y; Rodenburg, M; Williams, G; Adam, N; Berry, E; Elmer, P; Gerbaudo, D; Halyo, V; Hebda, P; Hunt, A; Jones, J; Laird, E; Lopes Pegna, D; Marlow, D; Medvedeva, T; Mooney, M; Olsen, J; Piroué, P; Saka, H; Stickland, D; Tully, C; Werner, J S; Zuranski, A; Acosta, J G; Huang, X T; Lopez, A; Mendez, H; Oliveros, S; Vargas, J E Ramirez; Zatserklyaniy, A; Alagoz, E; Barnes, V E; Bolla, G; Borrello, L; Bortoletto, D; Everett, A; Garfinkel, A F; Gecse, Z; Gutay, L; Jones, M; Koybasi, O; Laasanen, A T; Leonardo, N; Liu, C; Maroussov, V; Meier, M; Merkel, P; Miller, D H; Neumeister, N; Potamianos, K; Shipsey, I; Silvers, D; Svyatkovskiy, A; Yoo, H D; Zablocki, J; Zheng, Y; Jindal, P; Parashar, N; Boulahouache, C; Cuplov, V; Ecklund, K M; Geurts, F J M; Liu, J H; Morales, J; Padley, B P; Redjimi, R; Roberts, J; Zabel, J; Betchart, B; Bodek, A; Chung, Y S; de Barbaro, P; Demina, R; Eshaq, Y; Flacher, H; Garcia-Bellido, A; Goldenzweig, P; Gotra, Y; Han, J; Harel, A; Miner, D C; Orbaker, D; Petrillo, G; Vishnevskiy, D; Zielinski, M; Bhatti, A; Demortier, L; Goulianos, K; Lungu, G; Mesropian, C; Yan, M; Atramentov, O; Barker, A; Duggan, D; Gershtein, Y; Gray, R; Halkiadakis, E; Hidas, D; Hits, D; Lath, A; Panwalkar, S; Patel, R; Richards, A; Rose, K; Schnetzer, S; Somalwar, S; Stone, R; Thomas, S; Cerizza, G; Hollingsworth, M; Spanier, S; Yang, Z C; York, A; Asaadi, J; Eusebi, R; Gilmore, J; Gurrola, A; Kamon, T; Khotilovich, V; Montalvo, R; Nguyen, C N; Pivarski, J; Safonov, A; Sengupta, S; Tatarinov, A; Toback, D; Weinberger, M; Akchurin, N; Bardak, C; Damgov, J; Jeong, C; Kovitanggoon, K; Lee, S W; Mane, P; Roh, Y; Sill, A; Volobouev, I; Wigmans, R; Yazgan, E; Appelt, E; Brownson, E; Engh, D; Florez, C; Gabella, W; Johns, W; Kurt, P; Maguire, C; Melo, A; Sheldon, P; Velkovska, J; Arenton, M W; Balazs, M; Boutle, S; Buehler, M; Conetti, S; Cox, B; Francis, B; Hirosky, R; Ledovskoy, A; Lin, C; Neu, C; Patel, T; Yohay, R; Gollapinni, S; Harr, R; Karchin, P E; Mattson, M; Milstène, C; Sakharov, A; Anderson, M; Bachtis, M; Bellinger, J N; Carlsmith, D; Dasu, S; Efron, J; Gray, L; Grogg, K S; Grothe, M; Hall-Wilton, R; Herndon, M; Klabbers, P; Klukas, J; Lanaro, A; Lazaridis, C; Leonard, J; Liu, J; Lomidze, D; Loveless, R; Mohapatra, A; Parker, W; Reeder, D; Ross, I; Savin, A; Smith, W H; Swanson, J; Weinberg, M

2010-12-31

A search for quark compositeness in the form of quark contact interactions, based on hadronic jet pairs (dijets) produced in proton-proton collisions at √s=7 TeV, is described. The data sample of the study corresponds to an integrated luminosity of 2.9 pb(-1) collected with the CMS detector at the LHC. The dijet centrality ratio, which quantifies the angular distribution of the dijets, is measured as a function of the invariant mass of the dijet system and is found to agree with the predictions of the standard model. A statistical analysis of the data provides a lower limit on the energy scale of quark contact interactions. The sensitivity of the analysis is such that the expected limit is 2.9 TeV; because the observed value of the centrality ratio at high invariant mass is below the expectation, the observed limit is 4.0 TeV at the 95% confidence level.

Femtoscopy with identified charged pions in proton-lead collisions at s NN = 5.02 TeV with ATLAS

DOE PAGES

Aaboud, M.; Aad, G.; Abbott, B.; ...

2017-12-28

Here, Bose-Einstein correlations between identified charged pions are measured for p+Pb collisions at √ sNN = 5.02TeV using data recorded by the ATLAS detector at the CERN Large Hadron Collider corresponding to a total integrated luminosity of 28nb –1. Pions are identified using ionization energy loss measured in the pixel detector. Two-particle correlation functions and the extracted source radii are presented as a function of collision centrality as well as the average transverse momentum (k T) and rapidity (y* ππ) of the pair. Pairs are selected with a rapidity –2 < y* ππ < 1 and with an average transversemore » momentum 0.1 < k T < 0.8GeV. The effect of jet fragmentation on the two-particle correlation function is studied, and a method using opposite-charge pair data to constrain its contributions to the measured correlations is described. The measured source sizes are substantially larger in more central collisions and are observed to decrease with increasing pair k T. A correlation of the radii with the local charged-particle density is demonstrated. The scaling of the extracted radii with the mean number of participating nucleons is also used to compare a selection of initial-geometry models. The cross term Rol is measured as a function of rapidity, and a nonzero value is observed with 5.1σ combined significance for –1 < y* ππ < 1 in the most central events.« less

Differentiation of Enhancing Glioma and Primary Central Nervous System Lymphoma by Texture-Based Machine Learning.

PubMed

Alcaide-Leon, P; Dufort, P; Geraldo, A F; Alshafai, L; Maralani, P J; Spears, J; Bharatha, A

2017-06-01

Accurate preoperative differentiation of primary central nervous system lymphoma and enhancing glioma is essential to avoid unnecessary neurosurgical resection in patients with primary central nervous system lymphoma. The purpose of the study was to evaluate the diagnostic performance of a machine-learning algorithm by using texture analysis of contrast-enhanced T1-weighted images for differentiation of primary central nervous system lymphoma and enhancing glioma. Seventy-one adult patients with enhancing gliomas and 35 adult patients with primary central nervous system lymphomas were included. The tumors were manually contoured on contrast-enhanced T1WI, and the resulting volumes of interest were mined for textural features and subjected to a support vector machine-based machine-learning protocol. Three readers classified the tumors independently on contrast-enhanced T1WI. Areas under the receiver operating characteristic curves were estimated for each reader and for the support vector machine classifier. A noninferiority test for diagnostic accuracy based on paired areas under the receiver operating characteristic curve was performed with a noninferiority margin of 0.15. The mean areas under the receiver operating characteristic curve were 0.877 (95% CI, 0.798-0.955) for the support vector machine classifier; 0.878 (95% CI, 0.807-0.949) for reader 1; 0.899 (95% CI, 0.833-0.966) for reader 2; and 0.845 (95% CI, 0.757-0.933) for reader 3. The mean area under the receiver operating characteristic curve of the support vector machine classifier was significantly noninferior to the mean area under the curve of reader 1 ( P = .021), reader 2 ( P = .035), and reader 3 ( P = .007). Support vector machine classification based on textural features of contrast-enhanced T1WI is noninferior to expert human evaluation in the differentiation of primary central nervous system lymphoma and enhancing glioma. © 2017 by American Journal of Neuroradiology.

Report on Pairing-based Cryptography.

PubMed

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

2015-01-01

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

Report on Pairing-based Cryptography

PubMed Central

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

2015-01-01

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

The hidden treasures of long-term paired watershed monitoring in the forests and grasslands of Arizona, USA

Treesearch

B. Poff; D. G. Neary; V. Henderson; A. Tecle

2012-01-01

Beginning in the 1950s, researchers of the United States Department of Agriculture Forest Service established a series of paired watershed studies throughout north-central and eastern Arizona. A total of nine experimental watershed areas were established in the pinyon-juniper and chaparral woodlands, as well as the ponderosa pine and mixed conifer forests. While most...

The Presence of Thermally Unstable X-Ray Filaments and the Production of Cold Gas in the NGC 5044 Group

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

David, Laurence P.; Vrtilek, Jan; O’Sullivan, Ewan

We present the results of a deep Chandra observation of the X-ray bright moderate-cooling flow group NGC 5044 along with the observed correlations between the ionized, atomic, and molecular gas in this system. The Chandra observation shows that the central AGN has undergone two outbursts in the past 10{sup 8} years, based on the presence of two pairs of nearly bipolar X-ray cavities. The molecular gas and dust within the central 2 kpc is aligned with the orientation of the inner pair of bipolar X-ray cavities, suggesting that the most recent AGN outburst had a dynamical impact on the molecularmore » gas. NGC 5044 also hosts many X-ray filaments within the central 8 kpc, but there are no obvious connections between the X-ray and H α filaments and the more extended X-ray cavities that were inflated during the prior AGN outburst. Using the line width of the blended Fe-L line complex as a diagnostic for multiphase gas, we find that the majority of the multiphase thermally unstable gas in NGC 5044 is confined within the X-ray filaments. While the cooling time and entropy of the gas within the X-ray filaments are very similar, not all filaments show evidence of gas cooling or an association with H α emission. We suggest that the various observed properties of the X-ray filaments are suggestive of an evolutionary sequence where thermally unstable gas begins to cool, becomes multiphased, develops H α emitting plasma, and finally produces cold gas.« less

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

PubMed Central

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

2015-01-01

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

Transposon Tn10 contains two structural genes with opposite polarity between tetA and IS10R.

PubMed Central

Schollmeier, K; Hillen, W

1984-01-01

The nucleotide sequence of the central part of Tn10 has been determined from the rightmost HindIII site to IS10R. This sequence contains two open reading frames with opposite polarity. The in vivo transcription start points in this sequence have been determined by S1 mapping. These results define one minor and two major promoters. The transcription starts of the two major promoters are only 18 base pairs apart, and the transcripts show different polarity and overlap by 18 base pairs. The nucleotide sequence reveals two regions with palindromic symmetry which may serve as operators. Their possible involvement in the regulation of transcription of both genes is discussed. Taken together these results allow for a maximal coding capacity of 138 amino acids directed toward IS10R and 197 amino acids directed toward tetA. The possible function of these gene products is discussed. The accompanying article (Braus et al., J. Bacteriol. 160:504-509, 1984) presents evidence that these genes are expressed. Images PMID:6094471

Pyrvinium pamoate changes alternative splicing of the serotonin receptor 2C by influencing its RNA structure

PubMed Central

Shen, Manli; Bellaousov, Stanislav; Hiller, Michael; de La Grange, Pierre; Creamer, Trevor P.; Malina, Orit; Sperling, Ruth; Mathews, David H.; Stoilov, Peter; Stamm, Stefan

2013-01-01

The serotonin receptor 2C plays a central role in mood and appetite control. It undergoes pre-mRNA editing as well as alternative splicing. The RNA editing suggests that the pre-mRNA forms a stable secondary structure in vivo. To identify substances that promote alternative exons inclusion, we set up a high-throughput screen and identified pyrvinium pamoate as a drug-promoting exon inclusion without editing. Circular dichroism spectroscopy indicates that pyrvinium pamoate binds directly to the pre-mRNA and changes its structure. SHAPE (selective 2′-hydroxyl acylation analysed by primer extension) assays show that part of the regulated 5′-splice site forms intramolecular base pairs that are removed by this structural change, which likely allows splice site recognition and exon inclusion. Genome-wide analyses show that pyrvinium pamoate regulates >300 alternative exons that form secondary structures enriched in A–U base pairs. Our data demonstrate that alternative splicing of structured pre-mRNAs can be regulated by small molecules that directly bind to the RNA, which is reminiscent to an RNA riboswitch. PMID:23393189

Modelling the secular evolution of migrating planet pairs

NASA Astrophysics Data System (ADS)

Michtchenko, T. A.; Rodríguez, A.

2011-08-01

The subject of this paper is the secular behaviour of a pair of planets evolving under dissipative forces. In particular, we investigate the case when dissipative forces affect the planetary semimajor axes and the planets move inwards/outwards the central star, in a process known as planet migration. To perform this investigation, we introduce fundamental concepts of conservative and dissipative dynamics of the three-body problem. Based on these concepts, we develop a qualitative model of the secular evolution of the migrating planetary pair. Our approach is based on the analysis of the energy and the orbital angular momentum exchange between the two-planet system and an external medium; thus no specific kind of dissipative forces is invoked. We show that, under the assumption that dissipation is weak and slow, the evolutionary routes of the migrating planets are traced by the Mode I and Mode II stationary solutions of the conservative secular problem. The ultimate convergence and the evolution of the system along one of these secular modes of motion are determined uniquely by the condition that the dissipation rate is sufficiently smaller than the proper secular frequency of the system. We show that it is possible to reassemble the starting configurations and the migration history of the systems on the basis of their final states and consequently to constrain the parameters of the physical processes involved.

External jugular venous pressure as an alternative to conventional central venous pressure in right lobe donor hepatectomies.

PubMed

Abdullah, Mohamed Hussein; Soliman, Hossam El Deen; Morad, Wessam Saber

2011-12-01

Many centers have adopted central vein cannulation both for central venous pressure monitoring and fluid administration for right hepatectomy in living-liver donors. However, use of central venous catheters is associated with adverse events that are hazardous to patients and expensive to treat. This study sought to examine the use of external jugular venous pressure as an alternative to conventional central venous pressure in right lobe donor hepatectomies Forty ASA grade I adult living liver-donors without a known history of significant cardiac or pulmonary diseases were enrolled in this prospective observational study. Paired measurement of venous pressures (external jugular venous pressure and internal jugular venous pressure) were taken at the following times: after induction of anesthesia, 30 minutes after skin incision, during right lobe mobilization (every 15 minutes), during hepatic transaction (every 15 minutes), after right lobe resection (every 15 minutes), and after abdominal closure. Paired measurements were equal in 47.5%, 53.5%, 61.5%, 46.3%, and 52.5% for after induction, after skin incision, right lobe mobilization, right lobe transection, after resection, and before abdominal closure periods. However, all measurements were within acceptable limits of bias measurements (± 2 mm Hg). Central venous pressure catheter placement can be avoided and replaced by a less-invasive method such as external jugular venous pressure (which gave an acceptable estimate of central venous pressure in all phases of right lobe resection) in living-donor liver transplant and allowed equivalent monitor even during fluid restriction phases.

Post-traumatic stress avoidance is attenuated by corticosterone and associated with brain levels of steroid receptor co-activator-1 in rats.

PubMed

Whitaker, Annie M; Farooq, Muhammad A; Edwards, Scott; Gilpin, Nicholas W

2016-01-01

Individuals with post-traumatic stress disorder (PTSD) avoid trauma-related stimuli and exhibit blunted hypothalamic-pituitary-adrenal (HPA) axis activation at the time of stress. Our rodent model of stress mimics the avoidance symptom cluster of PTSD. Rats are classified as "Avoiders" or "Non-Avoiders" post-stress based on the avoidance of a predator-odor paired context. Previously, we found Avoiders exhibit an attenuated HPA stress response to predator odor. We hypothesized that corticosterone administration before stress would reduce the magnitude and incidence of stress-paired context avoidance. Furthermore, we also predicted that Avoiders would exhibit altered expression of glucocorticoid receptor (GR) signaling machinery elements, including steroid receptor co-activator (SRC)-1. Male Wistar rats (n = 16) were pretreated with corticosterone (25 mg/kg) or saline and exposed to predator-odor stress paired with a context and tested for avoidance 24 h later. A second group of corticosterone-naïve rats (n = 24) were stressed (or not), indexed for avoidance 24 h later, and killed 48 h post-odor exposure to measure phosphorylated GR, FKBP51 and SRC-1 levels in the paraventricular nucleus (PVN), central amygdala (CeA) and ventral hippocampus (VH), all brain sites that highly express GRs and regulate HPA function. Corticosterone pretreatment reduced the magnitude and incidence of avoidance. In Avoiders, predator-odor exposure led to lower SRC-1 expression in the PVN and CeA, and higher SRC-1 expression in the VH. SRC-1 expression in PVN, CeA and VH was predicted by prior avoidance behavior. Hence, a blunted HPA stress response may contribute to stress-induced neuroadaptations in central SRC-1 levels and behavioral dysfunction in Avoider rats.

Accuracy of Cirrus HD-OCT and Topcon SP-3000P for measuring central corneal thickness.

PubMed

Calvo-Sanz, Jorge A; Ruiz-Alcocer, Javier; Sánchez-Tena, Miguel A

2017-02-18

To compare and analyze the interchangeability of three measuring systems, each based on a different technique, for central corneal thickness (CCT) analysis. CCT measurements were measured using optical coherence tomography (OCT), non-contact specular microscopy (NCSM), and ultrasonic pachymetry (USP) in 60 eyes of 60 healthy patients with a mean age of 66.5±15.0 years and a mean spherical equivalent of 0.43±1.14 D. Analysis of variations in measurement concordance and correlation among the three different methods were performed. Comparison of CCT measurements were done using Bland-Altman plots (with bias and 95% confidence intervals), intraclass correlation coefficient (ICC), and paired t-student analysis. Mean CCT values were: 549.20±26.91μm for USP (range 503-618μm), 514.20±27.49μm for NCSM (range 456-586μm) and 542.80±25.56μm for OCT (range 486-605μm). CCT values obtained with NCMS were significantly lower than those obtained with OCT and USP methods. NCMS CCT value was 36.08±10.72μm lower than USP value (p<0.05), and NCMS CCT value was 7.88±8.86μm lower than OCT value (p<0.05). ICC between USP-NCSM pair was 0.488 and 0.909 between USP-OCT pair. OCT and UPS offered highly comparable results, whereas NCSM offered lower mean CCT values compared to the other two methods. Therefore, NCSM should not be considered a reliable method for measuring CCT and should rather be considered for assessing longitudinal changes in the same patient. Copyright © 2017 Spanish General Council of Optometry. Published by Elsevier España, S.L.U. All rights reserved.

Hop stunt viroid: molecular cloning and nucleotide sequence of the complete cDNA copy.

PubMed Central

Ohno, T; Takamatsu, N; Meshi, T; Okada, Y

1983-01-01

The complete cDNA of hop stunt viroid (HSV) has been cloned by the method of Okayama and Berg (Mol.Cell.Biol.2,161-170. (1982] and the complete nucleotide sequence has been established. The covalently closed circular single-stranded HSV RNA consists of 297 nucleotides. The secondary structure predicted for HSV contains 67% of its residues base-paired. The native HSV can possess an extended rod-like structure characteristic of viroids previously established. The central region of the native HSV has a similar structure to the conserved region found in all viroids sequenced so far except for avocado sunblotch viroid. The sequence homologous to the 5'-end of U1a RNA is also found in the sequence of HSV but not in the central conserved region. Images PMID:6312412

Nucleic acid duplexes incorporating a dissociable covalent base pair

NASA Technical Reports Server (NTRS)

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

1999-01-01

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

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

PubMed

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

2015-11-02

Metallo-base pairs have been extensively studied for applications in nucleic acid-based nanodevices and genetic code expansion. Metallo-base pairs composed of natural nucleobases are attractive because nanodevices containing natural metallo-base pairs can be easily prepared from commercially available sources. Previously, we have reported a crystal structure of a DNA duplex containing T-Hg(II)-T base pairs. Herein, we have determined a high-resolution crystal structure of the second natural metallo-base pair between pyrimidine bases C-Ag(I)-C formed in an RNA duplex. One Ag(I) occupies the center between two cytosines and forms a C-Ag(I)-C base pair through N3-Ag(I)-N3 linear coordination. The C-Ag(I)-C base pair formation does not disturb the standard A-form conformation of RNA. Since the C-Ag(I)-C base pair is structurally similar to the canonical Watson-Crick base pairs, it can be a useful building block for structure-based design and fabrication of nucleic acid-based nanodevices. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Asymmetrical bonding in cold spraying of dissimilar materials

NASA Astrophysics Data System (ADS)

Nikbakht, R.; Seyedein, S. H.; Kheirandish, S.; Assadi, H.; Jodoin, B.

2018-06-01

Characteristics of particle bonding, especially for dissimilar materials, remains a key question in cold spray deposition. There are limited reports in direct correlation to particle/substrate bonding and peripheral shear zones. Cold spraying experiments and numerical simulations are conducted to characterise and analyse the correlation between bonding and peripheral shear zones for asymmetric particle/substrate pairs of intermetallic-forming elements of nickel and titanium. The correlation between metallic bonding and highly strained areas is explored in view of the growth of the intermetallic phase at the particle/substrate interface during subsequent heat treatments. Characterisation of the as-sprayed samples reveal that for the Ni(particle)/Ti(substrate) pair, plastic deformation of the particle is dominating over substrate deformation. However, for the Ti(particle)/Ni(substrate) pair, it is observed that the substrate and particle deform to similar extents. Characterisation of the samples after a brief heat treatment at 700 °C indicate that intermetallic formation, and hence metallurgical bonding of the pairs is more likely to occur at the particle peripheries where the interface areas are highly strained, and rarely achieved at the particle base. Results also reveal that bonding extends from peripheries toward the central part of the interfaces with increasing the impact velocity. The kinetics of interfacial intermetallic formation at peripheral areas and its correlation to particle bonding is discussed in view of deformation-enhanced interdiffusion.

A tachykinin-like neuroendocrine signalling axis couples central serotonin action and nutrient sensing with peripheral lipid metabolism

PubMed Central

Palamiuc, Lavinia; Noble, Tallie; Witham, Emily; Ratanpal, Harkaranveer; Vaughan, Megan; Srinivasan, Supriya

2017-01-01

Serotonin, a central neuromodulator with ancient ties to feeding and metabolism, is a major driver of body fat loss. However, mechanisms by which central serotonin action leads to fat loss remain unknown. Here, we report that the FLP-7 neuropeptide and its cognate receptor, NPR-22, function as the ligand-receptor pair that defines the neuroendocrine axis of serotonergic body fat loss in Caenorhabditis elegans. FLP-7 is secreted as a neuroendocrine peptide in proportion to fluctuations in neural serotonin circuit functions, and its release is regulated from secretory neurons via the nutrient sensor AMPK. FLP-7 acts via the NPR-22/Tachykinin2 receptor in the intestine and drives fat loss via the adipocyte triglyceride lipase ATGL-1. Importantly, this ligand-receptor pair does not alter other serotonin-dependent behaviours including food intake. For global modulators such as serotonin, the use of distinct neuroendocrine peptides for each output may be one means to achieve phenotypic selectivity. PMID:28128367

Josephson Parametric Amplifer Based on a Cavity-Embedded Cooper Pair Transistor

NASA Astrophysics Data System (ADS)

Li, Juliang; Rimberg, A. J.

In this experiment a cavity-embedded Cooper-pair transistor (cCPT) is used as a Josephson parametric amplifier. The cCPT consists of a Cooper pair transistor placed at the voltage antinode of a 5.7 GHz shorted quarter-wave resonator so that the CPT provides a galvanic connection between the cavity's central conductor and ground plane, which forms a SQUID loop. Both the flux threading the loop as well as the gate charge can be modulated, and each can provide the parametric pumping. The reflected signal from the cCPT is further amplified by both SLUG and HEMT amplifiers for characterizing the parametric amplification. A first application of the parametric amplification is to improve the charge sensitivity of a single electron charge detector. This can be done either by pumping on a side band or by shifting the charge state of the cCPT near a bifurcation point. Stimulated emission has been also observed when the cCPT is pumped at twice the resonant frequency in the absence of an input signal. This could allow investigation of the dynamic Casimir effect as well as generation of non-classical photon states. Supported by Grants ARO W911NF-13-10377 and NSF DMR 1507400.

Molecular cytogenetic map of the central bearded dragon, Pogona vitticeps (Squamata: Agamidae).

PubMed

Young, M J; O'Meally, D; Sarre, S D; Georges, A; Ezaz, T

2013-07-01

Reptiles, as the sister group to birds and mammals, are particularly valuable for comparative genomic studies among amniotes. The Australian central bearded dragon (Pogona vitticeps) is being developed as a reptilian model for such comparisons, with whole-genome sequencing near completion. The karyotype consists of 6 pairs of macrochromosomes and 10 pairs microchromosomes (2n = 32), including a female heterogametic ZW sex microchromosome pair. Here, we present a molecular cytogenetic map for P. vitticeps comprising 87 anchor bacterial artificial chromosome clones that together span each macro- and microchromosome. It is the first comprehensive cytogenetic map for any non-avian reptile. We identified an active nucleolus organizer region (NOR) on the sub-telomeric region of 2q by mapping 18S rDNA and Ag-NOR staining. We identified interstitial telomeric sequences in two microchromosome pairs and the W chromosome, indicating that microchromosome fusion has been a mechanism of karyotypic evolution in Australian agamids within the last 21 to 19 million years. Orthology searches against the chicken genome revealed an intrachromosomal rearrangement of P. vitticeps 1q, identified regions orthologous to chicken Z on P. vitticeps 2q, snake Z on P. vitticeps 6q and the autosomal microchromosome pair in P. vitticeps orthologous to turtle Pelodiscus sinensis ZW and lizard Anolis carolinensis XY. This cytogenetic map will be a valuable reference tool for future gene mapping studies and will provide the framework for the work currently underway to physically anchor genome sequences to chromosomes for this model Australian squamate.

Photoactive devices including porphyrinoids with coordinating additives

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

Forrest, Stephen R; Zimmerman, Jeramy; Yu, Eric K

Coordinating additives are included in porphyrinoid-based materials to promote intermolecular organization and improve one or more photoelectric characteristics of the materials. The coordinating additives are selected from fullerene compounds and organic compounds having free electron pairs. Combinations of different coordinating additives can be used to tailor the characteristic properties of such porphyrinoid-based materials, including porphyrin oligomers. Bidentate ligands are one type of coordinating additive that can form coordination bonds with a central metal ion of two different porphyrinoid compounds to promote porphyrinoid alignment and/or pi-stacking. The coordinating additives can shift the absorption spectrum of a photoactive material toward higher wavelengths,more » increase the external quantum efficiency of the material, or both.« less

The DEAH-box helicase Dhr1 dissociates U3 from the pre-rRNA to promote formation of the central pseudoknot.

PubMed

Sardana, Richa; Liu, Xin; Granneman, Sander; Zhu, Jieyi; Gill, Michael; Papoulas, Ophelia; Marcotte, Edward M; Tollervey, David; Correll, Carl C; Johnson, Arlen W

2015-02-01

In eukaryotes, the highly conserved U3 small nucleolar RNA (snoRNA) base-pairs to multiple sites in the pre-ribosomal RNA (pre-rRNA) to promote early cleavage and folding events. Binding of the U3 box A region to the pre-rRNA is mutually exclusive with folding of the central pseudoknot (CPK), a universally conserved rRNA structure of the small ribosomal subunit essential for protein synthesis. Here, we report that the DEAH-box helicase Dhr1 (Ecm16) is responsible for displacing U3. An active site mutant of Dhr1 blocked release of U3 from the pre-ribosome, thereby trapping a pre-40S particle. This particle had not yet achieved its mature structure because it contained U3, pre-rRNA, and a number of early-acting ribosome synthesis factors but noticeably lacked ribosomal proteins (r-proteins) that surround the CPK. Dhr1 was cross-linked in vivo to the pre-rRNA and to U3 sequences flanking regions that base-pair to the pre-rRNA including those that form the CPK. Point mutations in the box A region of U3 suppressed a cold-sensitive mutation of Dhr1, strongly indicating that U3 is an in vivo substrate of Dhr1. To support the conclusions derived from in vivo analysis we showed that Dhr1 unwinds U3-18S duplexes in vitro by using a mechanism reminiscent of DEAD box proteins.

The DEAH-box Helicase Dhr1 Dissociates U3 from the Pre-rRNA to Promote Formation of the Central Pseudoknot

PubMed Central

Granneman, Sander; Zhu, Jieyi; Gill, Michael; Papoulas, Ophelia; Marcotte, Edward M.; Tollervey, David; Correll, Carl C.; Johnson, Arlen W.

2015-01-01

In eukaryotes, the highly conserved U3 small nucleolar RNA (snoRNA) base-pairs to multiple sites in the pre-ribosomal RNA (pre-rRNA) to promote early cleavage and folding events. Binding of the U3 box A region to the pre-rRNA is mutually exclusive with folding of the central pseudoknot (CPK), a universally conserved rRNA structure of the small ribosomal subunit essential for protein synthesis. Here, we report that the DEAH-box helicase Dhr1 (Ecm16) is responsible for displacing U3. An active site mutant of Dhr1 blocked release of U3 from the pre-ribosome, thereby trapping a pre-40S particle. This particle had not yet achieved its mature structure because it contained U3, pre-rRNA, and a number of early-acting ribosome synthesis factors but noticeably lacked ribosomal proteins (r-proteins) that surround the CPK. Dhr1 was cross-linked in vivo to the pre-rRNA and to U3 sequences flanking regions that base-pair to the pre-rRNA including those that form the CPK. Point mutations in the box A region of U3 suppressed a cold-sensitive mutation of Dhr1, strongly indicating that U3 is an in vivo substrate of Dhr1. To support the conclusions derived from in vivo analysis we showed that Dhr1 unwinds U3-18S duplexes in vitro by using a mechanism reminiscent of DEAD box proteins. PMID:25710520

Solution structure of a DNA duplex containing a cis-diammineplatinum(II) 1,3-d(GTG) intrastrand cross-link, a major adduct in cells treated with the anticancer drug carboplatin.

PubMed

Teuben, J M; Bauer, C; Wang, A H; Reedijk, J

1999-09-21

The platinum 1,3-d(GXG) intrastrand cross-link is one of the adducts formed in the reaction of the antitumor drug cisplatin with DNA, and in fact the major adduct found in cells treated with the cisplatin analogue carboplatin. To determine the 3D structure of this adduct, the duplex d(CTCTGTGTCTC).d(GAGACACAGAG)], where GTG denotes a platinum 1,3-intrastrand cross-link, was prepared and studied with high-resolution (1)H NMR. The solution structure was determined using the SPEDREF protocol, which includes an iterative NOE-restrained refinement procedure. Calculated and recorded NOE spectra were found to be in good agreement (NMR R factor 22%). The studied duplex is more distorted from B-DNA than previously determined structures of the 1,2-d(GG) intrastrand adducts. The base pairing is lost for the 5'G-C and the central T-A base pair in the GTG lesion, and the central thymine is extruded from the minor groove. To accommodate this lesion, the minor groove is widened, and the 5'-guanine ribose adopts an N-type conformation. The helix is unwound locally and is significantly bent toward the major groove. Significant difference between the structural distortion of the 1, 3-d(GTG) cross-link and other Pt-DNA cross-links sheds new light on the observed differences in protein recognition of these lesions, and thus on the possible differences in mechanisms of action of the various Pt-DNA adducts formed in treatment with platinum anticancer complexes.

Structure of homeodomain-leucine zipper/DNA complexes studied using hydroxyl radical cleavage of DNA and methylation interference.

PubMed

Tron, Adriana E; Comelli, Raúl N; Gonzalez, Daniel H

2005-12-27

Homeodomain-leucine zipper (HD-Zip) proteins, unlike most homeodomain proteins, bind a pseudopalindromic DNA sequence as dimers. We have investigated the structure of the DNA complexes formed by two HD-Zip proteins with different nucleotide preferences at the central position of the binding site using footprinting and interference methods. The results indicate that the respective complexes are not symmetric, with the strand bearing a central purine (top strand) showing higher protection around the central region and the bottom strand protected toward the 3' end. Binding to a sequence with a nonpreferred central base pair produces a decrease in protection in either the top or the bottom strand, depending upon the protein. Modeling studies derived from the complex formed by the monomeric Antennapedia homeodomain with DNA indicate that in the HD-Zip/DNA complex the recognition helix of one of the monomers is displaced within the major groove respective to the other one. This monomer seems to lose contacts with a part of the recognition sequence upon binding to the nonpreferred site. The results show that the structure of the complex formed by HD-Zip proteins with DNA is dependent upon both protein intrinsic characteristics and the nucleotides present at the central position of the recognition sequence.

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

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

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

PubMed

Petrenko, Y M

2015-01-01

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

Nucleic acid duplexes incorporating a dissociable covalent base pair

PubMed Central

Gao, Kui; Orgel, Leslie E.

1999-01-01

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

Diagnostic significance of intrathecally produced herpes simplex and varizella-zoster virus-specific antibodies in central nervous system infections.

PubMed

Schultze, Detlev; Weder, Bruno; Cassinotti, Pascal; Vitek, Lucie; Krausse, Konrad; Fierz, Walter

2004-11-27

The optimal strategy for the diagnosis of herpes simplex virus (HSV) and varizella-zoster virus (VZV) disease of the central nervous system is the detection of viral DNA by polymerase chain reaction assay (PCR) in cerebrospinal fluid (CSF) and the examination of intrathecal production of specific antibodies. However, in acute neurological disease caused by either HSV or VZV, dual intrathecal synthesis of HSV-1, 2- as well as VZV-specific antibodies may be detectable and thus can hamper accurate aetiological diagnosis. This paper illustrates such equivocal findings in two case reports, investigates their frequency and discusses the possible reasons. Consecutive CSF/serum pairs of two patients with central nervous system (CNS) disease were tested by HSV-1-, HSV-2-, and VZV-specific PCR and by different serological assays for detection of neurotropic viruses and bacteria. Additionally, the results of microbiological investigations of 1'155 CSF/serum samples were retrospectively analyzed for coincident intrathecal antibody synthesis against HSV-1, 2 and VZV. Although only HSV-1 and VZV-specific DNA was detectable in the CSF of two patients with encephalitis and chronic meningitis, respectively, increasing intrathecal antibody production against both virus species could be demonstrated. Retrospective analysis of 1155 CSF/serum pairs revealed 55 (4.8%) pairs with evidence for intrathecally produced antibodies against either HSV-1, 2 (30/55) or VZV (14/55). Eleven of these 55 (20%) pairs showed intrathecal antibody-production against both virus species. Patients with CNS infection with HSV and VZV can be diagnosed by detecting intrathecally produced virus-specific antibodies, in addition to virus-specific PCR. However, in an appreciable proportion of patients a correct diagnosis is hampered by coincidentally detected antibodies in CSF against both virus species. Possible reasons for these equivocal findings are given.

Testing comparative phylogeographic models of marine vicariance and dispersal using a hierarchical Bayesian approach

PubMed Central

2008-01-01

Background Marine allopatric speciation is an enigma because pelagic larval dispersal can potentially connect disjunct populations thereby preventing reproductive and morphological divergence. Here we present a new hierarchical approximate Bayesian computation model (HABC) that tests two hypotheses of marine allopatric speciation: 1.) "soft vicariance", where a speciation involves fragmentation of a large widespread ancestral species range that was previously connected by long distance gene flow; and 2.) peripatric colonization, where speciations in peripheral archipelagos emerge from sweepstakes colonizations from central source regions. The HABC approach analyzes all the phylogeographic datasets at once in order to make across taxon-pair inferences about biogeographic processes while explicitly allowing for uncertainty in the demographic differences within each taxon-pair. Our method uses comparative phylogeographic data that consists of single locus mtDNA sequences from multiple co-distributed taxa containing pairs of central and peripheral populations. We use the method on two comparative phylogeographic data sets consisting of cowrie gastropod endemics co-distributed in the Hawaiian (11 taxon-pairs) and Marquesan archipelagos (7 taxon-pairs). Results Given the Marquesan data, we find strong evidence of simultaneous colonization across all seven cowrie gastropod endemics co-distributed in the Marquesas. In contrast, the lower sample sizes in the Hawaiian data lead to greater uncertainty associated with the Hawaiian estimates. Although, the hyper-parameter estimates point to soft vicariance in a subset of the 11 Hawaiian taxon-pairs, the hyper-prior and hyper-posterior are too similar to make a definitive conclusion. Both results are not inconsistent with what is known about the geologic history of the archipelagos. Simulations verify that our method can successfully distinguish these two histories across a wide range of conditions given sufficient sampling. Conclusion Although soft vicariance and colonization are likely to produce similar genetic patterns when a single taxon-pair is used, our hierarchical Bayesian model can potentially detect if either history is a dominant process across co-distributed taxon-pairs. As comparative phylogeographic datasets grow to include > 100 co-distributed taxon-pairs, the HABC approach will be well suited to dissect temporal patterns in community assembly and evolution, thereby providing a bridge linking comparative phylogeography with community ecology. PMID:19038027

Centrality Dependence of the Charged-Particle Multiplicity Density at Midrapidity in Pb-Pb Collisions at √{sN N }=5.02 TeV

NASA Astrophysics Data System (ADS)

Adam, J.; Adamová, D.; Aggarwal, M. M.; Aglieri Rinella, G.; Agnello, M.; Agrawal, N.; Ahammed, Z.; Ahmad, S.; Ahn, S. U.; Aiola, S.; Akindinov, A.; Alam, S. N.; Aleksandrov, D.; Alessandro, B.; Alexandre, D.; Alfaro Molina, R.; Alici, A.; Alkin, A.; Almaraz, J. R. M.; Alme, J.; Alt, T.; Altinpinar, S.; Altsybeev, I.; Alves Garcia Prado, C.; Andrei, C.; Andronic, A.; Anguelov, V.; Antičić, T.; Antinori, F.; Antonioli, P.; Aphecetche, L.; Appelshäuser, H.; Arcelli, S.; Arnaldi, R.; Arnold, O. W.; Arsene, I. C.; Arslandok, M.; Audurier, B.; Augustinus, A.; Averbeck, R.; Azmi, M. D.; Badalà, A.; Baek, Y. W.; Bagnasco, S.; Bailhache, R.; Bala, R.; Balasubramanian, S.; Baldisseri, A.; Baral, R. C.; Barbano, A. M.; Barbera, R.; Barile, F.; Barnaföldi, G. G.; Barnby, L. S.; Barret, V.; Bartalini, P.; Barth, K.; Bartke, J.; Bartsch, E.; Basile, M.; Bastid, N.; Basu, S.; Bathen, B.; Batigne, G.; Batista Camejo, A.; Batyunya, B.; Batzing, P. C.; Bearden, I. G.; Beck, H.; Bedda, C.; Behera, N. K.; Belikov, I.; Bellini, F.; Bello Martinez, H.; Bellwied, R.; Belmont, R.; Belmont-Moreno, E.; Belyaev, V.; Benacek, P.; Bencedi, G.; Beole, S.; Berceanu, I.; Bercuci, A.; Berdnikov, Y.; Berenyi, D.; Bertens, R. A.; Berzano, D.; Betev, L.; Bhasin, A.; Bhat, I. R.; Bhati, A. K.; Bhattacharjee, B.; Bhom, J.; Bianchi, L.; Bianchi, N.; Bianchin, C.; Bielčík, J.; Bielčíková, J.; Bilandzic, A.; Biro, G.; Biswas, R.; Biswas, S.; Bjelogrlic, S.; Blair, J. T.; Blau, D.; Blume, C.; Bock, F.; Bogdanov, A.; Bøggild, H.; Boldizsár, L.; Bombara, M.; Book, J.; Borel, H.; Borissov, A.; Borri, M.; Bossú, F.; Botta, E.; Bourjau, C.; Braun-Munzinger, P.; Bregant, M.; Breitner, T.; Broker, T. A.; Browning, T. A.; Broz, M.; Brucken, E. J.; Bruna, E.; Bruno, G. E.; Budnikov, D.; Buesching, H.; Bufalino, S.; Buncic, P.; Busch, O.; Buthelezi, Z.; Butt, J. B.; Buxton, J. T.; Caffarri, D.; Cai, X.; Caines, H.; Calero Diaz, L.; Caliva, A.; Calvo Villar, E.; Camerini, P.; Carena, F.; Carena, W.; Carnesecchi, F.; Castillo Castellanos, J.; Castro, A. J.; Casula, E. A. R.; Ceballos Sanchez, C.; Cerello, P.; Cerkala, J.; Chang, B.; Chapeland, S.; Chartier, M.; Charvet, J. L.; Chattopadhyay, S.; Chattopadhyay, S.; Chauvin, A.; Chelnokov, V.; Cherney, M.; Cheshkov, C.; Cheynis, B.; Chibante Barroso, V.; Chinellato, D. D.; Cho, S.; Chochula, P.; Choi, K.; Chojnacki, M.; Choudhury, S.; Christakoglou, P.; Christensen, C. H.; Christiansen, P.; Chujo, T.; Chung, S. U.; Cicalo, C.; Cifarelli, L.; Cindolo, F.; Cleymans, J.; Colamaria, F.; Colella, D.; Collu, A.; Colocci, M.; Conesa Balbastre, G.; Conesa Del Valle, Z.; Connors, M. E.; Contreras, J. G.; Cormier, T. M.; Corrales Morales, Y.; Cortés Maldonado, I.; Cortese, P.; Cosentino, M. R.; Costa, F.; Crochet, P.; Cruz Albino, R.; Cuautle, E.; Cunqueiro, L.; Dahms, T.; Dainese, A.; Danisch, M. C.; Danu, A.; Das, D.; Das, I.; Das, S.; Dash, A.; Dash, S.; de, S.; de Caro, A.; de Cataldo, G.; de Conti, C.; de Cuveland, J.; de Falco, A.; de Gruttola, D.; De Marco, N.; de Pasquale, S.; Deisting, A.; Deloff, A.; Dénes, E.; Deplano, C.; Dhankher, P.; di Bari, D.; di Mauro, A.; di Nezza, P.; Diaz Corchero, M. A.; Dietel, T.; Dillenseger, P.; Divià, R.; Djuvsland, Ø.; Dobrin, A.; Domenicis Gimenez, D.; Dönigus, B.; Dordic, O.; Drozhzhova, T.; Dubey, A. K.; Dubla, A.; Ducroux, L.; Dupieux, P.; Ehlers, R. J.; Elia, D.; Endress, E.; Engel, H.; Epple, E.; Erazmus, B.; Erdemir, I.; Erhardt, F.; Espagnon, B.; Estienne, M.; Esumi, S.; Eum, J.; Evans, D.; Evdokimov, S.; Eyyubova, G.; Fabbietti, L.; Fabris, D.; Faivre, J.; Fantoni, A.; Fasel, M.; Feldkamp, L.; Feliciello, A.; Feofilov, G.; Ferencei, J.; Fernández Téllez, A.; Ferreiro, E. G.; Ferretti, A.; Festanti, A.; Feuillard, V. J. G.; Figiel, J.; Figueredo, M. A. S.; Filchagin, S.; Finogeev, D.; Fionda, F. M.; Fiore, E. M.; Fleck, M. G.; Floris, M.; Foertsch, S.; Foka, P.; Fokin, S.; Fragiacomo, E.; Francescon, A.; Frankenfeld, U.; Fronze, G. G.; Fuchs, U.; Furget, C.; Furs, A.; Fusco Girard, M.; Gaardhøje, J. J.; Gagliardi, M.; Gago, A. M.; Gallio, M.; Gangadharan, D. R.; Ganoti, P.; Gao, C.; Garabatos, C.; Garcia-Solis, E.; Gargiulo, C.; Gasik, P.; Gauger, E. F.; Germain, M.; Gheata, A.; Gheata, M.; Ghosh, P.; Ghosh, S. K.; Gianotti, P.; Giubellino, P.; Giubilato, P.; Gladysz-Dziadus, E.; Glässel, P.; Goméz Coral, D. M.; Gomez Ramirez, A.; Gonzalez, V.; González-Zamora, P.; Gorbunov, S.; Görlich, L.; Gotovac, S.; Grabski, V.; Grachov, O. A.; Graczykowski, L. K.; Graham, K. L.; Grelli, A.; Grigoras, A.; Grigoras, C.; Grigoriev, V.; Grigoryan, A.; Grigoryan, S.; Grinyov, B.; Grion, N.; Gronefeld, J. M.; Grosse-Oetringhaus, J. F.; Grossiord, J.-Y.; Grosso, R.; Guber, F.; Guernane, R.; Guerzoni, B.; Gulbrandsen, K.; Gunji, T.; Gupta, A.; Gupta, R.; Haake, R.; Haaland, Ø.; Hadjidakis, C.; Haiduc, M.; Hamagaki, H.; Hamar, G.; Hamon, J. C.; Harris, J. W.; Harton, A.; Hatzifotiadou, D.; Hayashi, S.; Heckel, S. T.; Helstrup, H.; Herghelegiu, A.; Herrera Corral, G.; Hess, B. A.; Hetland, K. F.; Hillemanns, H.; Hippolyte, B.; Horak, D.; Hosokawa, R.; Hristov, P.; Huang, M.; Humanic, T. J.; Hussain, N.; Hussain, T.; Hutter, D.; Hwang, D. S.; Ilkaev, R.; Inaba, M.; Incani, E.; Ippolitov, M.; Irfan, M.; Ivanov, M.; Ivanov, V.; Izucheev, V.; Jacazio, N.; Jacobs, P. M.; Jadhav, M. B.; Jadlovska, S.; Jadlovsky, J.; Jahnke, C.; Jakubowska, M. J.; Jang, H. J.; Janik, M. A.; Jayarathna, P. H. S. Y.; Jena, C.; Jena, S.; Jimenez Bustamante, R. T.; Jones, P. G.; Jusko, A.; Kalinak, P.; Kalweit, A.; Kamin, J.; Kang, J. H.; Kaplin, V.; Kar, S.; Karasu Uysal, A.; Karavichev, O.; Karavicheva, T.; Karayan, L.; Karpechev, E.; Kebschull, U.; Keidel, R.; Keijdener, D. L. D.; Keil, M.; Mohisin Khan, M.; Khan, P.; Khan, S. A.; Khanzadeev, A.; Kharlov, Y.; Kileng, B.; Kim, D. W.; Kim, D. J.; Kim, D.; Kim, H.; Kim, J. S.; Kim, M.; Kim, S.; Kim, T.; Kirsch, S.; Kisel, I.; Kiselev, S.; Kisiel, A.; Kiss, G.; Klay, J. L.; Klein, C.; Klein, J.; Klein-Bösing, C.; Klewin, S.; Kluge, A.; Knichel, M. L.; Knospe, A. G.; Kobdaj, C.; Kofarago, M.; Kollegger, T.; Kolojvari, A.; Kondratiev, V.; Kondratyeva, N.; Kondratyuk, E.; Konevskikh, A.; Kopcik, M.; Kostarakis, P.; Kour, M.; Kouzinopoulos, C.; Kovalenko, O.; Kovalenko, V.; Kowalski, M.; Koyithatta Meethaleveedu, G.; Králik, I.; Kravčáková, A.; Kretz, M.; Krivda, M.; Krizek, F.; Kryshen, E.; Krzewicki, M.; Kubera, A. M.; Kučera, V.; Kuhn, C.; Kuijer, P. G.; Kumar, A.; Kumar, J.; Kumar, L.; Kumar, S.; Kurashvili, P.; Kurepin, A.; Kurepin, A. B.; Kuryakin, A.; Kweon, M. J.; Kwon, Y.; La Pointe, S. L.; La Rocca, P.; Ladron de Guevara, P.; Lagana Fernandes, C.; Lakomov, I.; Langoy, R.; Lara, C.; Lardeux, A.; Lattuca, A.; Laudi, E.; Lea, R.; Leardini, L.; Lee, G. R.; Lee, S.; Lehas, F.; Lemmon, R. C.; Lenti, V.; Leogrande, E.; León Monzón, I.; León Vargas, H.; Leoncino, M.; Lévai, P.; Li, S.; Li, X.; Lien, J.; Lietava, R.; Lindal, S.; Lindenstruth, V.; Lippmann, C.; Lisa, M. A.; Ljunggren, H. M.; Lodato, D. F.; Loenne, P. I.; Loginov, V.; Loizides, C.; Lopez, X.; López Torres, E.; Lowe, A.; Luettig, P.; Lunardon, M.; Luparello, G.; Lutz, T. H.; Maevskaya, A.; Mager, M.; Mahajan, S.; Mahmood, S. M.; Maire, A.; Majka, R. D.; Malaev, M.; Maldonado Cervantes, I.; Malinina, L.; Mal'Kevich, D.; Malzacher, P.; Mamonov, A.; Manko, V.; Manso, F.; Manzari, V.; Marchisone, M.; Mareš, J.; Margagliotti, G. V.; Margotti, A.; Margutti, J.; Marín, A.; Markert, C.; Marquard, M.; Martin, N. A.; Martin Blanco, J.; Martinengo, P.; Martínez, M. I.; Martínez García, G.; Martinez Pedreira, M.; Mas, A.; Masciocchi, S.; Masera, M.; Masoni, A.; Massacrier, L.; Mastroserio, A.; Matyja, A.; Mayer, C.; Mazer, J.; Mazzoni, M. A.; McDonald, D.; Meddi, F.; Melikyan, Y.; Menchaca-Rocha, A.; Meninno, E.; Mercado Pérez, J.; Meres, M.; Miake, Y.; Mieskolainen, M. M.; Mikhaylov, K.; Milano, L.; Milosevic, J.; Minervini, L. M.; Mischke, A.; Mishra, A. N.; Miśkowiec, D.; Mitra, J.; Mitu, C. M.; Mohammadi, N.; Mohanty, B.; Molnar, L.; Montaño Zetina, L.; Montes, E.; Moreira de Godoy, D. A.; Moreno, L. A. P.; Moretto, S.; Morreale, A.; Morsch, A.; Muccifora, V.; Mudnic, E.; Mühlheim, D.; Muhuri, S.; Mukherjee, M.; Mulligan, J. D.; Munhoz, M. G.; Munzer, R. H.; Murakami, H.; Murray, S.; Musa, L.; Musinsky, J.; Naik, B.; Nair, R.; Nandi, B. K.; Nania, R.; Nappi, E.; Naru, M. U.; Natal da Luz, H.; Nattrass, C.; Navarro, S. R.; Nayak, K.; Nayak, R.; Nayak, T. K.; Nazarenko, S.; Nedosekin, A.; Nellen, L.; Ng, F.; Nicassio, M.; Niculescu, M.; Niedziela, J.; Nielsen, B. S.; Nikolaev, S.; Nikulin, S.; Nikulin, V.; Noferini, F.; Nomokonov, P.; Nooren, G.; Noris, J. C. C.; Norman, J.; Nyanin, A.; Nystrand, J.; Oeschler, H.; Oh, S.; Oh, S. K.; Ohlson, A.; Okatan, A.; Okubo, T.; Olah, L.; Oleniacz, J.; Oliveira da Silva, A. C.; Oliver, M. H.; Onderwaater, J.; Oppedisano, C.; Orava, R.; Ortiz Velasquez, A.; Oskarsson, A.; Otwinowski, J.; Oyama, K.; Ozdemir, M.; Pachmayer, Y.; Pagano, P.; Paić, G.; Pal, S. K.; Pan, J.; Pandey, A. K.; Papikyan, V.; Pappalardo, G. S.; Pareek, P.; Park, W. J.; Parmar, S.; Passfeld, A.; Paticchio, V.; Patra, R. N.; Paul, B.; Pei, H.; Peitzmann, T.; Pereira da Costa, H.; Peresunko, D.; Pérez Lara, C. E.; Perez Lezama, E.; Peskov, V.; Pestov, Y.; Petráček, V.; Petrov, V.; Petrovici, M.; Petta, C.; Piano, S.; Pikna, M.; Pillot, P.; Pimentel, L. O. D. L.; Pinazza, O.; Pinsky, L.; Piyarathna, D. 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E.; Sekiguchi, Y.; Sekihata, D.; Selyuzhenkov, I.; Senosi, K.; Senyukov, S.; Serradilla, E.; Sevcenco, A.; Shabanov, A.; Shabetai, A.; Shadura, O.; Shahoyan, R.; Shangaraev, A.; Sharma, A.; Sharma, M.; Sharma, M.; Sharma, N.; Shigaki, K.; Shtejer, K.; Sibiriak, Y.; Siddhanta, S.; Sielewicz, K. M.; Siemiarczuk, T.; Silvermyr, D.; Silvestre, C.; Simatovic, G.; Simonetti, G.; Singaraju, R.; Singh, R.; Singha, S.; Singhal, V.; Sinha, B. C.; Sinha, T.; Sitar, B.; Sitta, M.; Skaali, T. B.; Slupecki, M.; Smirnov, N.; Snellings, R. J. M.; Snellman, T. W.; Søgaard, C.; Song, J.; Song, M.; Song, Z.; Soramel, F.; Sorensen, S.; de Souza, R. D.; Sozzi, F.; Spacek, M.; Spiriti, E.; Sputowska, I.; Spyropoulou-Stassinaki, M.; Stachel, J.; Stan, I.; Stankus, P.; Stefanek, G.; Stenlund, E.; Steyn, G.; Stiller, J. H.; Stocco, D.; Strmen, P.; Suaide, A. A. 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S.; Zhalov, M.; Zhang, H.; Zhang, X.; Zhang, Y.; Zhang, C.; Zhang, Z.; Zhao, C.; Zhigareva, N.; Zhou, D.; Zhou, Y.; Zhou, Z.; Zhu, H.; Zhu, J.; Zichichi, A.; Zimmermann, A.; Zimmermann, M. B.; Zinovjev, G.; Zyzak, M.; Alice Collaboration

2016-06-01

The pseudorapidity density of charged particles, d Nch/d η , at midrapidity in Pb-Pb collisions has been measured at a center-of-mass energy per nucleon pair of √{sN N}=5.02 TeV . For the 5% most central collisions, we measure a value of 1943 ±54 . The rise in d Nch/d η as a function of √{sN N} is steeper than that observed in proton-proton collisions and follows the trend established by measurements at lower energy. The increase of d Nch/d η as a function of the average number of participant nucleons, ⟨Npart⟩ , calculated in a Glauber model, is compared with the previous measurement at √{sN N}=2.76 TeV . A constant factor of about 1.2 describes the increase in d Nch/d η from √{sN N}=2.76 to 5.02 TeV for all centrality classes, within the measured range of 0%-80% centrality. The results are also compared to models based on different mechanisms for particle production in nuclear collisions.

Centrality Dependence of the Charged-Particle Multiplicity Density at Midrapidity in Pb-Pb Collisions at sqrt[s_{NN}]=5.02  TeV.

PubMed

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Menchaca-Rocha, A; Meninno, E; Mercado Pérez, J; Meres, M; Miake, Y; Mieskolainen, M M; Mikhaylov, K; Milano, L; Milosevic, J; Minervini, L M; Mischke, A; Mishra, A N; Miśkowiec, D; Mitra, J; Mitu, C M; Mohammadi, N; Mohanty, B; Molnar, L; Montaño Zetina, L; Montes, E; Moreira De Godoy, D A; Moreno, L A P; Moretto, S; Morreale, A; Morsch, A; Muccifora, V; Mudnic, E; Mühlheim, D; Muhuri, S; Mukherjee, M; Mulligan, J D; Munhoz, M G; Munzer, R H; Murakami, H; Murray, S; Musa, L; Musinsky, J; Naik, B; Nair, R; Nandi, B K; Nania, R; Nappi, E; Naru, M U; Natal da Luz, H; Nattrass, C; Navarro, S R; Nayak, K; Nayak, R; Nayak, T K; Nazarenko, S; Nedosekin, A; Nellen, L; Ng, F; Nicassio, M; Niculescu, M; Niedziela, J; Nielsen, B S; Nikolaev, S; Nikulin, S; Nikulin, V; Noferini, F; Nomokonov, P; Nooren, G; Noris, J C C; Norman, J; Nyanin, A; Nystrand, J; Oeschler, H; Oh, S; Oh, S K; Ohlson, A; Okatan, A; Okubo, T; Olah, L; Oleniacz, J; Oliveira Da Silva, A C; Oliver, M H; Onderwaater, J; Oppedisano, C; Orava, R; Ortiz Velasquez, A; Oskarsson, A; Otwinowski, J; Oyama, K; Ozdemir, M; Pachmayer, Y; Pagano, P; Paić, G; Pal, S K; Pan, J; Pandey, A K; Papikyan, V; Pappalardo, G S; Pareek, P; Park, W J; Parmar, S; Passfeld, A; Paticchio, V; Patra, R N; Paul, B; Pei, H; Peitzmann, T; Pereira Da Costa, H; Peresunko, D; Pérez Lara, C E; Perez Lezama, E; Peskov, V; Pestov, Y; Petráček, V; Petrov, V; Petrovici, M; Petta, C; Piano, S; Pikna, M; Pillot, P; Pimentel, L O D L; Pinazza, O; Pinsky, L; Piyarathna, D B; Płoskoń, M; Planinic, M; Pluta, J; Pochybova, S; Podesta-Lerma, P L M; Poghosyan, M G; Polichtchouk, B; Poljak, N; Poonsawat, W; Pop, A; Porteboeuf-Houssais, S; Porter, J; Pospisil, J; Prasad, S K; Preghenella, R; Prino, F; Pruneau, C A; Pshenichnov, I; Puccio, M; Puddu, G; Pujahari, P; Punin, V; Putschke, J; Qvigstad, H; Rachevski, A; Raha, S; Rajput, S; Rak, J; Rakotozafindrabe, A; Ramello, L; Rami, F; Raniwala, R; Raniwala, S; Räsänen, S S; Rascanu, B T; Rathee, D; Read, K F; Redlich, K; 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Shabanov, A; Shabetai, A; Shadura, O; Shahoyan, R; Shangaraev, A; Sharma, A; Sharma, M; Sharma, M; Sharma, N; Shigaki, K; Shtejer, K; Sibiriak, Y; Siddhanta, S; Sielewicz, K M; Siemiarczuk, T; Silvermyr, D; Silvestre, C; Simatovic, G; Simonetti, G; Singaraju, R; Singh, R; Singha, S; Singhal, V; Sinha, B C; Sinha, T; Sitar, B; Sitta, M; Skaali, T B; Slupecki, M; Smirnov, N; Snellings, R J M; Snellman, T W; Søgaard, C; Song, J; Song, M; Song, Z; Soramel, F; Sorensen, S; de Souza, R D; Sozzi, F; Spacek, M; Spiriti, E; Sputowska, I; Spyropoulou-Stassinaki, M; Stachel, J; Stan, I; Stankus, P; Stefanek, G; Stenlund, E; Steyn, G; Stiller, J H; Stocco, D; Strmen, P; Suaide, A A P; Sugitate, T; Suire, C; Suleymanov, M; Suljic, M; Sultanov, R; Šumbera, M; Szabo, A; Szanto de Toledo, A; Szarka, I; Szczepankiewicz, A; Szymanski, M; Tabassam, U; Takahashi, J; Tambave, G J; Tanaka, N; Tangaro, M A; Tarhini, M; Tariq, M; Tarzila, M G; Tauro, A; Tejeda Muñoz, G; Telesca, A; Terasaki, K; Terrevoli, C; Teyssier, B; Thäder, J; Thomas, D; Tieulent, R; Timmins, A R; Toia, A; Trogolo, S; Trombetta, G; Trubnikov, V; Trzaska, W H; Tsuji, T; Tumkin, A; Turrisi, R; Tveter, T S; Ullaland, K; Uras, A; Usai, G L; Utrobicic, A; Vajzer, M; Vala, M; Valencia Palomo, L; Vallero, S; Van Der Maarel, J; Van Hoorne, J W; van Leeuwen, M; Vanat, T; Vande Vyvre, P; Varga, D; Vargas, A; Vargyas, M; Varma, R; Vasileiou, M; Vasiliev, A; Vauthier, A; Vechernin, V; Veen, A M; Veldhoen, M; Velure, A; Venaruzzo, M; Vercellin, E; Vergara Limón, S; Vernet, R; Verweij, M; Vickovic, L; Viesti, G; Viinikainen, J; Vilakazi, Z; Villalobos Baillie, O; Villatoro Tello, A; Vinogradov, A; Vinogradov, L; Vinogradov, Y; Virgili, T; Vislavicius, V; Viyogi, Y P; Vodopyanov, A; Völkl, M A; Voloshin, K; Voloshin, S A; Volpe, G; von Haller, B; Vorobyev, I; Vranic, D; Vrláková, J; Vulpescu, B; Wagner, B; Wagner, J; Wang, H; Wang, M; Watanabe, D; Watanabe, Y; Weber, M; Weber, S G; Weiser, D F; Wessels, J P; Westerhoff, U; Whitehead, A M; Wiechula, J; Wikne, J; Wilk, G; Wilkinson, J; Williams, M C S; Windelband, B; Winn, M; Yang, H; Yang, P; Yano, S; Yasar, C; Yin, Z; Yokoyama, H; Yoo, I-K; Yoon, J H; Yurchenko, V; Yushmanov, I; Zaborowska, A; Zaccolo, V; Zaman, A; Zampolli, C; Zanoli, H J C; Zaporozhets, S; Zardoshti, N; Zarochentsev, A; Závada, P; Zaviyalov, N; Zbroszczyk, H; Zgura, I S; Zhalov, M; Zhang, H; Zhang, X; Zhang, Y; Zhang, C; Zhang, Z; Zhao, C; Zhigareva, N; Zhou, D; Zhou, Y; Zhou, Z; Zhu, H; Zhu, J; Zichichi, A; Zimmermann, A; Zimmermann, M B; Zinovjev, G; Zyzak, M

2016-06-03

The pseudorapidity density of charged particles, dN_{ch}/dη, at midrapidity in Pb-Pb collisions has been measured at a center-of-mass energy per nucleon pair of sqrt[s_{NN}]=5.02  TeV. For the 5% most central collisions, we measure a value of 1943±54. The rise in dN_{ch}/dη as a function of sqrt[s_{NN}] is steeper than that observed in proton-proton collisions and follows the trend established by measurements at lower energy. The increase of dN_{ch}/dη as a function of the average number of participant nucleons, ⟨N_{part}⟩, calculated in a Glauber model, is compared with the previous measurement at sqrt[s_{NN}]=2.76  TeV. A constant factor of about 1.2 describes the increase in dN_{ch}/dη from sqrt[s_{NN}]=2.76 to 5.02 TeV for all centrality classes, within the measured range of 0%-80% centrality. The results are also compared to models based on different mechanisms for particle production in nuclear collisions.

CENTERA: A Centralized Trust-Based Efficient Routing Protocol with Authentication for Wireless Sensor Networks †

PubMed Central

Tajeddine, Ayman; Kayssi, Ayman; Chehab, Ali; Elhajj, Imad; Itani, Wassim

2015-01-01

In this paper, we present CENTERA, a CENtralized Trust-based Efficient Routing protocol with an appropriate authentication scheme for wireless sensor networks (WSN). CENTERA utilizes the more powerful base station (BS) to gather minimal neighbor trust information from nodes and calculate the best routes after isolating different types of “bad” nodes. By periodically accumulating these simple local observations and approximating the nodes' battery lives, the BS draws a global view of the network, calculates three quality metrics—maliciousness, cooperation, and compatibility—and evaluates the Data Trust and Forwarding Trust values of each node. Based on these metrics, the BS isolates “bad”, “misbehaving” or malicious nodes for a certain period, and put some nodes on probation. CENTERA increases the node's bad/probation level with repeated “bad” behavior, and decreases it otherwise. Then it uses a very efficient method to distribute the routing information to “good” nodes. Based on its target environment, and if required, CENTERA uses an authentication scheme suitable for severely constrained nodes, ranging from the symmetric RC5 for safe environments under close administration, to pairing-based cryptography (PBC) for hostile environments with a strong attacker model. We simulate CENTERA using TOSSIM and verify its correctness and show some energy calculations. PMID:25648712

CENTERA: a centralized trust-based efficient routing protocol with authentication for wireless sensor networks.

PubMed

Tajeddine, Ayman; Kayssi, Ayman; Chehab, Ali; Elhajj, Imad; Itani, Wassim

2015-02-02

In this paper, we present CENTERA, a CENtralized Trust-based Efficient Routing protocol with an appropriate authentication scheme for wireless sensor networks (WSN). CENTERA utilizes the more powerful base station (BS) to gather minimal neighbor trust information from nodes and calculate the best routes after isolating different types of "bad" nodes. By periodically accumulating these simple local observations and approximating the nodes' battery lives, the BS draws a global view of the network, calculates three quality metrics-maliciousness, cooperation, and compatibility-and evaluates the Data Trust and Forwarding Trust values of each node. Based on these metrics, the BS isolates "bad", "misbehaving" or malicious nodes for a certain period, and put some nodes on probation. CENTERA increases the node's bad/probation level with repeated "bad" behavior, and decreases it otherwise. Then it uses a very efficient method to distribute the routing information to "good" nodes. Based on its target environment, and if required, CENTERA uses an authentication scheme suitable for severely constrained nodes, ranging from the symmetric RC5 for safe environments under close administration, to pairing-based cryptography (PBC) for hostile environments with a strong attacker model. We simulate CENTERA using TOSSIM and verify its correctness and show some energy calculations.

Stereo photo series for quantifying cerrado fuels in Central Brazil—volume I.

Treesearch

R.D. Ottmar; R.E. Vihnanek; H.S. Miranda; M.N. Sata; S.M. Andrade

2001-01-01

The first volume of the Cerrado photo series is a collection of sites that represent a range of physiognomic forms of the Cerrado in central Brazil including campo limpo, campo sujo, cerrado ralo, cerrado sensu stricto, and cerrado denso. Sites include wide-angle and stereo pair photographs supplemented with information on living and dead fuels,...

Ambient Noise Tomography of central Java, with Transdimensional Bayesian Inversion

NASA Astrophysics Data System (ADS)

Zulhan, Zulfakriza; Saygin, Erdinc; Cummins, Phil; Widiyantoro, Sri; Nugraha, Andri Dian; Luehr, Birger-G.; Bodin, Thomas

2014-05-01

Delineating the crustal structure of central Java is crucial for understanding its complex tectonic setting. However, seismic imaging of the strong heterogeneity typical of such a tectonically active region can be challenging, particularly in the upper crust where velocity contrasts are strongest and steep body wave ray-paths provide poor resolution. We have applied ambient noise cross correlation of pair stations in central Java, Indonesia by using the MERapi Amphibious EXperiment (MERAMEX) dataset. The data were collected between May to October 2004. We used 120 of 134 temporary seismic stations for about 150 days of observation, which covered central Java. More than 5000 Rayleigh wave Green's function were extracted by cross-correlating the noise simultaneously recorded at available station pairs. We applied a fully nonlinear 2D Bayesian inversion technique to the retrieved travel times. Features in the derived tomographic images correlate well with previous studies, and some shallow structures that were not evident in previous studies are clearly imaged with Ambient Noise Tomography. The Kendeng Basin and several active volcanoes appear with very low group velocities, and anomalies with relatively high velocities can be interpreted in terms of crustal sutures and/or surface geological features.

POLAR-UVI and other Coordinated Observations of a Traveling Convection Vortex Event Observed on 24 July 1996

NASA Technical Reports Server (NTRS)

Clauer, C. R.; Baker, J. B.; Ridley, A. J.; Sitar, R. J.; Papitashvili, V. O.; Cumnock, J.; Spann, J. F., Jr.; Brittnacher, M. J.; Parks, G. K.

1997-01-01

Coordinated analysis of data from the POLAR UVI instrument, ground magnetometers, incoherent scatter radar, solar wind monitors IMP-8 and WIND, and DMSP satellite is focused on a traveling convection vortex (TCV) event on 24 July 1966. Starting at 10:48 UT, ground magnetometers in Greenland and eastern Canada measure pulsations consistent with the passing overhead of a series of alternating TCV field-aligned current pairs. Sondrestrom incoherent scatter radar measures strong modulation of the strength and direction of ionospheric plasma flow, The magnetometer pulsations grow in magnitude over the next hour, peaking in intensity at 11:39 UT, at which time the UVI instrument measures a localized intensification of auroral emissions over central and western Greenland. Subsequent images show the intensification grow in strength and propagate westward (tailward) until approximately 11:58 UT at which time the emissions fade. These observations are consistent with the westward passage of two pairs of moderately intense TCVs over central Greenland followed by a third very intense TCV pair. The intensification of auroral emissions at 11:39 UT is associated with the trailing vortex of the third TCV pair, thought to be the result of an upward field-aligned current. Measurements of the solar wind suggest that a pressure change may be responsible for triggering the first two pairs of TCVS, and that a subsequent sudden change in orientation of the IMF may have produced the intensification of the third TCV pair and the associated aurora] brightening. DMSP particle data indicate that the TCVs occur on field lines which map to the boundary plasma sheet or outer edge of the low latitude boundary layer.

Optogenetic activation of the central amygdala generates addiction-like preference for reward.

PubMed

Tom, Rebecca L; Ahuja, Aarit; Maniates, Hannah; Freeland, Charlotte M; Robinson, Mike J F

2018-05-23

Drug and behavioural addictions are characterized by an intense and focused pursuit of a single reward above all others. Pursuit of the addictive reward is often compulsively sought despite adverse consequences and better alternative outcomes. Here, we explored the ability of the central amygdala (CeA) to powerfully bias choice, causing specific rewards to be almost compulsively preferred. Rats were trained on an operant choice task in which they could choose to respond on either of the two levers to receive a sucrose reward, one of which was paired with optogenetic stimulation of the CeA using channelrhodopsin-2 (ChR2). Rats developed an almost exclusive preference for the laser-paired reward over the otherwise equal unpaired reward. We found that this preference for stimulation-paired reward persists even when a much larger sucrose reward is offered as an alternative (contingency management) or when this preferred reward is paired with adverse consequences such as progressively larger electric foot shock, time delays or effort requirements. We also report that when challenged with foot shock, a small proportion of these animals (≈20%) retained an exclusive laser-paired reward preference, whereas others began to seek the alternate reward when the shock reached high levels. Lastly, we confirmed that optogenetic CeA stimulation was not independently rewarding if delivered in the absence of a paired sucrose reward. These results suggest a role for the CeA in focusing motivation and desire to excessive levels, generating addiction-like behaviour that persists in the face of more rewarding alternatives and adverse consequences. © 2018 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

Mismatch and G-Stack Modulated Probe Signals on SNP Microarrays

PubMed Central

Binder, Hans; Fasold, Mario; Glomb, Torsten

2009-01-01

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

Experimental Investigation of Triplet Correlation Approximations for Fluid Water.

PubMed

Pallewela, Gayani N; Ploetz, Elizabeth A; Smith, Paul E

2018-08-25

Triplet correlations play a central role in our understanding of fluids and their properties. Of particular interest is the relationship between the pair and triplet correlations. Here we use a combination of Fluctuation Solution Theory and experimental pair radial distribution functions to investigate the accuracy of the Kirkwood Superposition Approximation (KSA), as given by integrals over the relevant pair and triplet correlation functions, at a series of state points for pure water using only experimental quantities. The KSA performs poorly, in agreement with a variety of other studies. Several additional approximate relationships between the pair and triplet correlations in fluids are also investigated and generally provide good agreement for the fluid thermodynamics for regions of the phase diagram where the compressibility is small. A simple power law relationship between the pair and triplet fluctuations is particularly successful for state points displaying low to moderately high compressibilities.

A new species of Ornithodoros (Acari: Argasidae), parasite of Microlophus spp. (Reptilia: Tropiduridae) from northern Chile.

PubMed

Venzal, José M; Nava, Santiago; González-Acuña, Daniel; Mangold, Atilio J; Muñoz-Leal, Sebastián; Lado, Paula; Guglielmone, Alberto A

2013-02-01

A new species, Ornithodoros microlophi (Acari: Argasidae), belonging to the subgenus Alectorobius is described from larvae collected on the lizards Microlophus atacamensis (Donoso-Barros, 1966) and Microlophus quadrivittatus (Tschudi, 1845) (Squamata: Tropiduridae) in continental and insular localities from northern Chile. Larvae of O. microlophi can be distinguished from other Neotropical species of the genus Ornithodoros by a combination of the following characters, namely 10 pairs of ventral setae, venter with 6 pairs of sternal setae, dorsal plate pyriform, 19-21 pairs of dorsal setae (typically 20), 13 pairs are dorsolateral and 7 pairs are central, and hypostome with dental formula 4/4 in medial portion and apex pointed. Phylogenetic analysis of 16S rDNA sequences suggests that O. microlophi represents an independent lineage within Neotropical species of the Argasidae. Copyright © 2012 Elsevier GmbH. All rights reserved.

Defragged Binary I Ching Genetic Code Chromosomes Compared to Nirenberg’s and Transformed into Rotating 2D Circles and Squares and into a 3D 100% Symmetrical Tetrahedron Coupled to a Functional One to Discern Start From Non-Start Methionines through a Stella Octangula

PubMed Central

Castro-Chavez, Fernando

2012-01-01

Background Three binary representations of the genetic code according to the ancient I Ching of Fu-Xi will be presented, depending on their defragging capabilities by pairing based on three biochemical properties of the nucleic acids: H-bonds, Purine/Pyrimidine rings, and the Keto-enol/Amino-imino tautomerism, yielding the last pair a 32/32 single-strand self-annealed genetic code and I Ching tables. Methods Our working tool is the ancient binary I Ching's resulting genetic code chromosomes defragged by vertical and by horizontal pairing, reverse engineered into non-binaries of 2D rotating 4×4×4 circles and 8×8 squares and into one 3D 100% symmetrical 16×4 tetrahedron coupled to a functional tetrahedron with apical signaling and central hydrophobicity (codon formula: 4[1(1)+1(3)+1(4)+4(2)]; 5:5, 6:6 in man) forming a stella octangula, and compared to Nirenberg's 16×4 codon table (1965) pairing the first two nucleotides of the 64 codons in axis y. Results One horizontal and one vertical defragging had the start Met at the center. Two, both horizontal and vertical pairings produced two pairs of 2×8×4 genetic code chromosomes naturally arranged (M and I), rearranged by semi-introversion of central purines or pyrimidines (M' and I') and by clustering hydrophobic amino acids; their quasi-identity was disrupted by amino acids with odd codons (Met and Tyr pairing to Ile and TGA Stop); in all instances, the 64-grid 90° rotational ability was restored. Conclusions We defragged three I Ching representations of the genetic code while emphasizing Nirenberg's historical finding. The synthetic genetic code chromosomes obtained reflect the protective strategy of enzymes with a similar function, having both humans and mammals a biased G-C dominance of three H-bonds in the third nucleotide of their most used codons per amino acid, as seen in one chromosome of the i, M and M' genetic codes, while a two H-bond A-T dominance was found in their complementary chromosome, as seen in invertebrates and plants. The reverse engineering of chromosome I' into 2D rotating circles and squares was undertaken, yielding a 100% symmetrical 3D geometry which was coupled to a previously obtained genetic code tetrahedron in order to differentiate the start methionine from the methionine that is acting as a codifying non-start codon. PMID:23431415

Discovery of a [WO] central star in the planetary nebula Th 2-A

NASA Astrophysics Data System (ADS)

Weidmann, W. A.; Gamen, R.; Díaz, R. J.; Niemela, V. S.

2008-09-01

Context: About 2500 planetary nebulae are known in our Galaxy but only 224 have central stars with reported spectral types in the Strasbourg-ESO Catalogue of Galactic Planetary Nebulae (Acker et al. 1992; Acker et al. 1996). Aims: We have started an observational program aiming to increase the number of PN central stars with spectral classification. Methods: By means of spectroscopy and high resolution imaging, we identify the position and true nature of the central star. We carried out low resolution spectroscopic observations at CASLEO telescope, complemented with medium resolution spectroscopy performed at Gemini South and Magellan telescopes. Results: As a first outcome of this survey, we present for the first time the spectra of the central star of the PN Th 2-A. These spectra show emission lines of ionized C and O, typical in Wolf-Rayet stars. Conclusions: We identify the position of that central star, which is not the brightest one of the visual central pair. We classify it as of type [WO 3]pec, which is consistent with the high excitation and dynamical age of the nebula. Based on data collected at (i) the Complejo Astronómico El Leoncito (CASLEO), which is operated under agreement between the Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina y Universidades Nacionales de La Plata, Córdoba y San Juan, Argentina; (ii) the 6.5 m Magellan Telescopes at Las Campanas Observatory, Chile; (iii) the 8 m Gemini South Telescope, Chile.

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

PubMed

Kimoto, Michiko; Hirao, Ichiro

2017-10-20

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

“Click, Click, Cyclize”: A DOS Approach to Sultams Utilizing Vinyl Sulfonamide Linchpins

PubMed Central

Zhou, Aihua; Rayabarapu, Dinesh; Hanson, Paul R.

2009-01-01

A diversity-oriented synthesis (DOS) strategy termed “Click, Click, Cyclize” is reported. This approach relies on functional group (FG) pairing between a vinyl sulfonamide and an array of functional groups to synthesize skeletally diverse sultams. Several FG pairing pathways on central tertiary vinyl sulfonamide linchpins have been developed including intramolecular Heck, aza-Michael, ring-closing enyne metathesis, Pauson—Khand, and chemoselective oxidation/Baylis—Hillman reactions. PMID:19115841

Relative Modification of Prompt ψ (2 S ) and J /ψ Yields from p p to PbPb Collisions at √{sN N }=5.02 TeV

NASA Astrophysics Data System (ADS)

Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Asilar, E.; Bergauer, T.; Brandstetter, J.; Brondolin, E.; Dragicevic, M.; Erö, J.; Flechl, M.; Friedl, M.; Frühwirth, R.; Ghete, V. M.; Hartl, C.; Hörmann, N.; Hrubec, J.; Jeitler, M.; König, A.; Krätschmer, I.; Liko, D.; Matsushita, T.; Mikulec, I.; Rabady, D.; Rad, N.; Rahbaran, B.; Rohringer, H.; Schieck, J.; Strauss, J.; Waltenberger, W.; Wulz, C.-E.; Chekhovsky, V.; Dvornikov, O.; Dydyshka, Y.; Emeliantchik, I.; Litomin, A.; Makarenko, V.; Mossolov, V.; Stefanovitch, R.; Suarez Gonzalez, J.; Zykunov, V.; Shumeiko, N.; Alderweireldt, S.; De Wolf, E. A.; Janssen, X.; Lauwers, J.; Van De Klundert, M.; Van Haevermaet, H.; Van Mechelen, P.; Van Remortel, N.; Van Spilbeeck, A.; Abu Zeid, S.; Blekman, F.; D'Hondt, J.; Daci, N.; De Bruyn, I.; Deroover, K.; Lowette, S.; Moortgat, S.; Moreels, L.; Olbrechts, A.; Python, Q.; Skovpen, K.; Tavernier, S.; Van Doninck, W.; Van Mulders, P.; Van Parijs, I.; Brun, H.; Clerbaux, B.; De Lentdecker, G.; Delannoy, H.; Fasanella, G.; Favart, L.; Goldouzian, R.; Grebenyuk, A.; Karapostoli, G.; Lenzi, T.; Léonard, A.; Luetic, J.; Maerschalk, T.; Marinov, A.; Randle-conde, A.; Seva, T.; Vander Velde, C.; Vanlaer, P.; Vannerom, D.; Yonamine, R.; Zenoni, F.; Zhang, F.; Cimmino, A.; Cornelis, T.; Dobur, D.; Fagot, A.; Garcia, G.; Gul, M.; Khvastunov, I.; Poyraz, D.; Salva, S.; Schöfbeck, R.; Tytgat, M.; Van Driessche, W.; Yazgan, E.; Zaganidis, N.; Bakhshiansohi, H.; Beluffi, C.; Bondu, O.; Brochet, S.; Bruno, G.; Caudron, A.; De Visscher, S.; Delaere, C.; Delcourt, M.; Francois, B.; Giammanco, A.; Jafari, A.; Jez, P.; Komm, M.; Krintiras, G.; Lemaitre, V.; Magitteri, A.; Mertens, A.; Musich, M.; Nuttens, C.; Piotrzkowski, K.; Quertenmont, L.; Selvaggi, M.; Vidal Marono, M.; Wertz, S.; Beliy, N.; Aldá Júnior, W. L.; Alves, F. L.; Alves, G. A.; Brito, L.; Hensel, C.; Moraes, A.; Pol, M. E.; Rebello Teles, P.; Belchior Batista Das Chagas, E.; Carvalho, W.; Chinellato, J.; Custódio, A.; Da Costa, E. M.; Da Silveira, G. G.; De Jesus Damiao, D.; De Oliveira Martins, C.; Fonseca De Souza, S.; Huertas Guativa, L. M.; Malbouisson, H.; Matos Figueiredo, D.; Mora Herrera, C.; Mundim, L.; Nogima, H.; Prado Da Silva, W. L.; Santoro, A.; Sznajder, A.; Tonelli Manganote, E. J.; Vilela Pereira, A.; Ahuja, S.; Bernardes, C. A.; Dogra, S.; Tomei, T. R. Fernandez Perez; Gregores, E. M.; Mercadante, P. G.; Moon, C. S.; Novaes, S. F.; Padula, Sandra S.; Romero Abad, D.; Ruiz Vargas, J. C.; Aleksandrov, A.; Hadjiiska, R.; Iaydjiev, P.; Rodozov, M.; Stoykova, S.; Sultanov, G.; Vutova, M.; Dimitrov, A.; Glushkov, I.; Litov, L.; Pavlov, B.; Petkov, P.; Fang, W.; Ahmad, M.; Bian, J. G.; Chen, G. M.; Chen, H. S.; Chen, M.; Chen, Y.; Cheng, T.; Jiang, C. H.; Leggat, D.; Liu, Z.; Romeo, F.; Shaheen, S. M.; Spiezia, A.; Tao, J.; Wang, C.; Wang, Z.; Zhang, H.; Zhao, J.; Ban, Y.; Chen, G.; Li, Q.; Liu, S.; Mao, Y.; Qian, S. J.; Wang, D.; Xu, Z.; Avila, C.; Cabrera, A.; Chaparro Sierra, L. F.; Florez, C.; Gomez, J. P.; González Hernández, C. F.; Ruiz Alvarez, J. D.; Sanabria, J. C.; Godinovic, N.; Lelas, D.; Puljak, I.; Ribeiro Cipriano, P. M.; Sculac, T.; Antunovic, Z.; Kovac, M.; Brigljevic, V.; Ferencek, D.; Kadija, K.; Mesic, B.; Micanovic, S.; Sudic, L.; Susa, T.; Attikis, A.; Mavromanolakis, G.; Mousa, J.; Nicolaou, C.; Ptochos, F.; Razis, P. A.; Rykaczewski, H.; Tsiakkouri, D.; Finger, M.; Finger, M.; Carrera Jarrin, E.; Ellithi Kamel, A.; Mahmoud, M. A.; Radi, A.; Kadastik, M.; Perrini, L.; Raidal, M.; Tiko, A.; Veelken, C.; Eerola, P.; Pekkanen, J.; Voutilainen, M.; Härkönen, J.; Järvinen, T.; Karimäki, V.; Kinnunen, R.; Lampén, T.; Lassila-Perini, K.; Lehti, S.; Lindén, T.; Luukka, P.; Tuominiemi, J.; Tuovinen, E.; Wendland, L.; Talvitie, J.; Tuuva, T.; Besancon, M.; Couderc, F.; Dejardin, M.; Denegri, D.; Fabbro, B.; Faure, J. L.; Favaro, C.; Ferri, F.; Ganjour, S.; Ghosh, S.; Givernaud, A.; Gras, P.; Hamel de Monchenault, G.; Jarry, P.; Kucher, I.; Locci, E.; Machet, M.; Malcles, J.; Rander, J.; Rosowsky, A.; Titov, M.; Zghiche, A.; Abdulsalam, A.; Antropov, I.; Arleo, F.; Baffioni, S.; Beaudette, F.; Busson, P.; Cadamuro, L.; Chapon, E.; Charlot, C.; Davignon, O.; Granier de Cassagnac, R.; Jo, M.; Lisniak, S.; Martin Blanco, J.; Miné, P.; Nguyen, M.; Ochando, C.; Ortona, G.; Paganini, P.; Pigard, P.; Regnard, S.; Salerno, R.; Sirois, Y.; Stahl Leiton, A. G.; Strebler, T.; Yilmaz, Y.; Zabi, A.; Agram, J.-L.; Andrea, J.; Aubin, A.; Bloch, D.; Brom, J.-M.; Buttignol, M.; Chabert, E. C.; Chanon, N.; Collard, C.; Conte, E.; Coubez, X.; Fontaine, J.-C.; Gelé, D.; Goerlach, U.; Le Bihan, A.-C.; Van Hove, P.; Gadrat, S.; Beauceron, S.; Bernet, C.; Boudoul, G.; Carrillo Montoya, C. A.; Chierici, R.; Contardo, D.; Courbon, B.; Depasse, P.; El Mamouni, H.; Fan, J.; Fay, J.; Gascon, S.; Gouzevitch, M.; Grenier, G.; Ille, B.; Lagarde, F.; Laktineh, I. B.; Lethuillier, M.; Mirabito, L.; Pequegnot, A. L.; Perries, S.; Popov, A.; Sabes, D.; Sordini, V.; Vander Donckt, M.; Verdier, P.; Viret, S.; Toriashvili, T.; Tsamalaidze, Z.; Autermann, C.; Beranek, S.; Feld, L.; Kiesel, M. K.; Klein, K.; Lipinski, M.; Preuten, M.; Schael, S.; Schomakers, C.; Schulz, J.; Verlage, T.; Albert, A.; Brodski, M.; Dietz-Laursonn, E.; Duchardt, D.; Endres, M.; Erdmann, M.; Erdweg, S.; Esch, T.; Fischer, R.; Güth, A.; Hamer, M.; Hebbeker, T.; Heidemann, C.; Hoepfner, K.; Knutzen, S.; Merschmeyer, M.; Meyer, A.; Millet, P.; Mukherjee, S.; Olschewski, M.; Padeken, K.; Pook, T.; Radziej, M.; Reithler, H.; Rieger, M.; Scheuch, F.; Sonnenschein, L.; Teyssier, D.; Thüer, S.; Cherepanov, V.; Flügge, G.; Kargoll, B.; Kress, T.; Künsken, A.; Lingemann, J.; Müller, T.; Nehrkorn, A.; Nowack, A.; Pistone, C.; Pooth, O.; Stahl, A.; Aldaya Martin, M.; Arndt, T.; Asawatangtrakuldee, C.; Beernaert, K.; Behnke, O.; Behrens, U.; Bin Anuar, A. A.; Borras, K.; Campbell, A.; Connor, P.; Contreras-Campana, C.; Costanza, F.; Diez Pardos, C.; Dolinska, G.; Eckerlin, G.; Eckstein, D.; Eichhorn, T.; Eren, E.; Gallo, E.; Garay Garcia, J.; Geiser, A.; Gizhko, A.; Grados Luyando, J. M.; Grohsjean, A.; Gunnellini, P.; Harb, A.; Hauk, J.; Hempel, M.; Jung, H.; Kalogeropoulos, A.; Karacheban, O.; Kasemann, M.; Keaveney, J.; Kleinwort, C.; Korol, I.; Krücker, D.; Lange, W.; Lelek, A.; Leonard, J.; Lipka, K.; Lobanov, A.; Lohmann, W.; Mankel, R.; Melzer-Pellmann, I.-A.; Meyer, A. B.; Mittag, G.; Mnich, J.; Mussgiller, A.; Ntomari, E.; Pitzl, D.; Placakyte, R.; Raspereza, A.; Roland, B.; Sahin, M. Ö.; Saxena, P.; Schoerner-Sadenius, T.; Seitz, C.; Spannagel, S.; Stefaniuk, N.; Van Onsem, G. P.; Walsh, R.; Wissing, C.; Blobel, V.; Centis Vignali, M.; Draeger, A. R.; Dreyer, T.; Garutti, E.; Gonzalez, D.; Haller, J.; Hoffmann, M.; Junkes, A.; Klanner, R.; Kogler, R.; Kovalchuk, N.; Lapsien, T.; Lenz, T.; Marchesini, I.; Marconi, D.; Meyer, M.; Niedziela, M.; Nowatschin, D.; Pantaleo, F.; Peiffer, T.; Perieanu, A.; Poehlsen, J.; Sander, C.; Scharf, C.; Schleper, P.; Schmidt, A.; Schumann, S.; Schwandt, J.; Stadie, H.; Steinbrück, G.; Stober, F. M.; Stöver, M.; Tholen, H.; Troendle, D.; Usai, E.; Vanelderen, L.; Vanhoefer, A.; Vormwald, B.; Akbiyik, M.; Barth, C.; Baur, S.; Baus, C.; Berger, J.; Butz, E.; Caspart, R.; Chwalek, T.; Colombo, F.; De Boer, W.; Dierlamm, A.; Fink, S.; Freund, B.; Friese, R.; Giffels, M.; Gilbert, A.; Goldenzweig, P.; Haitz, D.; Hartmann, F.; Heindl, S. M.; Husemann, U.; Katkov, I.; Kudella, S.; Mildner, H.; Mozer, M. U.; Müller, Th.; Plagge, M.; Quast, G.; Rabbertz, K.; Röcker, S.; Roscher, F.; Schröder, M.; Shvetsov, I.; Sieber, G.; Simonis, H. J.; Ulrich, R.; Wayand, S.; Weber, M.; Weiler, T.; Williamson, S.; Wöhrmann, C.; Wolf, R.; Anagnostou, G.; Daskalakis, G.; Geralis, T.; Giakoumopoulou, V. A.; Kyriakis, A.; Loukas, D.; Topsis-Giotis, I.; Kesisoglou, S.; Panagiotou, A.; Saoulidou, N.; Tziaferi, E.; Evangelou, I.; Flouris, G.; Foudas, C.; Kokkas, P.; Loukas, N.; Manthos, N.; Papadopoulos, I.; Paradas, E.; Filipovic, N.; Bencze, G.; Hajdu, C.; Horvath, D.; Sikler, F.; Veszpremi, V.; Vesztergombi, G.; Zsigmond, A. J.; Beni, N.; Czellar, S.; Karancsi, J.; Makovec, A.; Molnar, J.; Szillasi, Z.; Bartók, M.; Raics, P.; Trocsanyi, Z. L.; Ujvari, B.; Bahinipati, S.; Choudhury, S.; Mal, P.; Mandal, K.; Nayak, A.; Sahoo, D. K.; Sahoo, N.; Swain, S. K.; Bansal, S.; Beri, S. B.; Bhatnagar, V.; Chawla, R.; Bhawandeep, U.; Kalsi, A. K.; Kaur, A.; Kaur, M.; Kumar, R.; Kumari, P.; Mehta, A.; Mittal, M.; Singh, J. B.; Walia, G.; Kumar, Ashok; Bhardwaj, A.; Choudhary, B. C.; Garg, R. B.; Keshri, S.; Malhotra, S.; Naimuddin, M.; Nishu, N.; Ranjan, K.; Sharma, R.; Sharma, V.; Bhattacharya, R.; Bhattacharya, S.; Chatterjee, K.; Dey, S.; Dutt, S.; Dutta, S.; Ghosh, S.; Majumdar, N.; Modak, A.; Mondal, K.; Mukhopadhyay, S.; Nandan, S.; Purohit, A.; Roy, A.; Roy, D.; Roy Chowdhury, S.; Sarkar, S.; Sharan, M.; Thakur, S.; Behera, P. K.; Chudasama, R.; Dutta, D.; Jha, V.; Kumar, V.; Mohanty, A. K.; Netrakanti, P. K.; Pant, L. M.; Shukla, P.; Topkar, A.; Aziz, T.; Dugad, S.; Kole, G.; Mahakud, B.; Mitra, S.; Mohanty, G. B.; Parida, B.; Sur, N.; Sutar, B.; Banerjee, S.; Bhowmik, S.; Dewanjee, R. K.; Ganguly, S.; Guchait, M.; Jain, Sa.; Kumar, S.; Maity, M.; Majumder, G.; Mazumdar, K.; Sarkar, T.; Wickramage, N.; Chauhan, S.; Dube, S.; Hegde, V.; Kapoor, A.; Kothekar, K.; Pandey, S.; Rane, A.; Sharma, S.; Chenarani, S.; Eskandari Tadavani, E.; Etesami, S. M.; Fahim, A.; Khakzad, M.; Mohammadi Najafabadi, M.; Naseri, M.; Paktinat Mehdiabadi, S.; Rezaei Hosseinabadi, F.; Safarzadeh, B.; Zeinali, M.; Felcini, M.; Grunewald, M.; Abbrescia, M.; Calabria, C.; Caputo, C.; Colaleo, A.; Creanza, D.; Cristella, L.; De Filippis, N.; De Palma, M.; Fiore, L.; Iaselli, G.; Maggi, G.; Maggi, M.; Miniello, G.; My, S.; Nuzzo, S.; Pompili, A.; Pugliese, G.; Radogna, R.; Ranieri, A.; Selvaggi, G.; Sharma, A.; Silvestris, L.; Venditti, R.; Verwilligen, P.; Abbiendi, G.; Battilana, C.; Bonacorsi, D.; Braibant-Giacomelli, S.; Brigliadori, L.; Campanini, R.; Capiluppi, P.; Castro, A.; Cavallo, F. R.; Chhibra, S. S.; Codispoti, G.; Cuffiani, M.; Dallavalle, G. M.; Fabbri, F.; Fanfani, A.; Fasanella, D.; Giacomelli, P.; Grandi, C.; Guiducci, L.; Marcellini, S.; Masetti, G.; Montanari, A.; Navarria, F. L.; Perrotta, A.; Rossi, A. M.; Rovelli, T.; Siroli, G. P.; Tosi, N.; Albergo, S.; Costa, S.; Di Mattia, A.; Giordano, F.; Potenza, R.; Tricomi, A.; Tuve, C.; Barbagli, G.; Ciulli, V.; Civinini, C.; D'Alessandro, R.; Focardi, E.; Lenzi, P.; Meschini, M.; Paoletti, S.; Sguazzoni, G.; Viliani, L.; Benussi, L.; Bianco, S.; Fabbri, F.; Piccolo, D.; Primavera, F.; Calvelli, V.; Ferro, F.; Lo Vetere, M.; Monge, M. R.; Robutti, E.; Tosi, S.; Brianza, L.; Brivio, F.; Dinardo, M. E.; Fiorendi, S.; Gennai, S.; Ghezzi, A.; Govoni, P.; Malberti, M.; Malvezzi, S.; Manzoni, R. A.; Menasce, D.; Moroni, L.; Paganoni, M.; Pedrini, D.; Pigazzini, S.; Ragazzi, S.; Tabarelli de Fatis, T.; Buontempo, S.; Cavallo, N.; De Nardo, G.; Di Guida, S.; Esposito, M.; Fabozzi, F.; Fienga, F.; Iorio, A. O. M.; Lanza, G.; Lista, L.; Meola, S.; Paolucci, P.; Sciacca, C.; Thyssen, F.; Azzi, P.; Bacchetta, N.; Benato, L.; Bisello, D.; Boletti, A.; Carlin, R.; Carvalho Antunes De Oliveira, A.; Checchia, P.; Dall'Osso, M.; De Castro Manzano, P.; Dorigo, T.; Dosselli, U.; Gasparini, F.; Gasparini, U.; Gozzelino, A.; Lacaprara, S.; Margoni, M.; Meneguzzo, A. T.; Pazzini, J.; Pozzobon, N.; Ronchese, P.; Simonetto, F.; Torassa, E.; Zanetti, M.; Zotto, P.; Zumerle, G.; Braghieri, A.; Magnani, A.; Montagna, P.; Ratti, S. P.; Re, V.; Riccardi, C.; Salvini, P.; Vai, I.; Vitulo, P.; Alunni Solestizi, L.; Bilei, G. M.; Ciangottini, D.; Fanò, L.; Lariccia, P.; Leonardi, R.; Mantovani, G.; Menichelli, M.; Saha, A.; Santocchia, A.; Androsov, K.; Azzurri, P.; Bagliesi, G.; Bernardini, J.; Boccali, T.; Castaldi, R.; Ciocci, M. A.; Dell'Orso, R.; Donato, S.; Fedi, G.; Giassi, A.; Grippo, M. T.; Ligabue, F.; Lomtadze, T.; Martini, L.; Messineo, A.; Palla, F.; Rizzi, A.; Savoy-Navarro, A.; Spagnolo, P.; Tenchini, R.; Tonelli, G.; Venturi, A.; Verdini, P. G.; Barone, L.; Cavallari, F.; Cipriani, M.; Del Re, D.; Diemoz, M.; Gelli, S.; Longo, E.; Margaroli, F.; Marzocchi, B.; Meridiani, P.; Organtini, G.; Paramatti, R.; Preiato, F.; Rahatlou, S.; Rovelli, C.; Santanastasio, F.; Amapane, N.; Arcidiacono, R.; Argiro, S.; Arneodo, M.; Bartosik, N.; Bellan, R.; Biino, C.; Cartiglia, N.; Cenna, F.; Costa, M.; Covarelli, R.; Degano, A.; Demaria, N.; Finco, L.; Kiani, B.; Mariotti, C.; Maselli, S.; Migliore, E.; Monaco, V.; Monteil, E.; Monteno, M.; Obertino, M. M.; Pacher, L.; Pastrone, N.; Pelliccioni, M.; Pinna Angioni, G. L.; Ravera, F.; Romero, A.; Ruspa, M.; Sacchi, R.; Shchelina, K.; Sola, V.; Solano, A.; Staiano, A.; Traczyk, P.; Belforte, S.; Casarsa, M.; Cossutti, F.; Della Ricca, G.; Zanetti, A.; Kim, D. H.; Kim, G. N.; Kim, M. S.; Lee, S.; Lee, S. W.; Oh, Y. D.; Sekmen, S.; Son, D. C.; Yang, Y. C.; Lee, A.; Kim, H.; Brochero Cifuentes, J. A.; Kim, T. J.; Cho, S.; Choi, S.; Go, Y.; Gyun, D.; Ha, S.; Hong, B.; Jo, Y.; Kim, Y.; Lee, B.; Lee, K.; Lee, K. S.; Lee, S.; Lim, J.; Park, S. K.; Roh, Y.; Almond, J.; Kim, J.; Lee, H.; Oh, S. B.; Radburn-Smith, B. C.; Seo, S. h.; Yang, U. K.; Yoo, H. D.; Yu, G. B.; Choi, M.; Kim, H.; Kim, J. H.; Lee, J. S. H.; Park, I. C.; Ryu, G.; Ryu, M. S.; Choi, Y.; Goh, J.; Hwang, C.; Lee, J.; Yu, I.; Dudenas, V.; Juodagalvis, A.; Vaitkus, J.; Ahmed, I.; Ibrahim, Z. A.; Komaragiri, J. R.; Md Ali, M. A. B.; Mohamad Idris, F.; Wan Abdullah, W. A. T.; Yusli, M. N.; Zolkapli, Z.; Castilla-Valdez, H.; De La Cruz-Burelo, E.; Heredia-De La Cruz, I.; Hernandez-Almada, A.; Lopez-Fernandez, R.; Magaña Villalba, R.; Mejia Guisao, J.; Sanchez-Hernandez, A.; Carrillo Moreno, S.; Oropeza Barrera, C.; Vazquez Valencia, F.; Carpinteyro, S.; Pedraza, I.; Salazar Ibarguen, H. A.; Uribe Estrada, C.; Morelos Pineda, A.; Krofcheck, D.; Butler, P. H.; Ahmad, A.; Ahmad, M.; Hassan, Q.; Hoorani, H. R.; Khan, W. A.; Saddique, A.; Shah, M. A.; Shoaib, M.; Waqas, M.; Bialkowska, H.; Bluj, M.; Boimska, B.; Frueboes, T.; Górski, M.; Kazana, M.; Nawrocki, K.; Romanowska-Rybinska, K.; Szleper, M.; Zalewski, P.; Bunkowski, K.; Byszuk, A.; Doroba, K.; Kalinowski, A.; Konecki, M.; Krolikowski, J.; Misiura, M.; Olszewski, M.; Walczak, M.; Bargassa, P.; Beirão Da Cruz E Silva, C.; Calpas, B.; Di Francesco, A.; Faccioli, P.; Ferreira Parracho, P. G.; Gallinaro, M.; Hollar, J.; Leonardo, N.; Lloret Iglesias, L.; Nemallapudi, M. V.; Rodrigues Antunes, J.; Seixas, J.; Toldaiev, O.; Vadruccio, D.; Varela, J.; Vischia, P.; Afanasiev, S.; Bunin, P.; Gavrilenko, M.; Golutvin, I.; Gorbunov, I.; Kamenev, A.; Karjavin, V.; Lanev, A.; Malakhov, A.; Matveev, V.; Palichik, V.; Perelygin, V.; Shmatov, S.; Shulha, S.; Skatchkov, N.; Smirnov, V.; Voytishin, N.; Zarubin, A.; Chtchipounov, L.; Golovtsov, V.; Ivanov, Y.; Kim, V.; Kuznetsova, E.; Murzin, V.; Oreshkin, V.; Sulimov, V.; Vorobyev, A.; Andreev, Yu.; Dermenev, A.; Gninenko, S.; Golubev, N.; Karneyeu, A.; Kirsanov, M.; Krasnikov, N.; Pashenkov, A.; Tlisov, D.; Toropin, A.; Epshteyn, V.; Gavrilov, V.; Lychkovskaya, N.; Popov, V.; Pozdnyakov, I.; Safronov, G.; Spiridonov, A.; Toms, M.; Vlasov, E.; Zhokin, A.; Bylinkin, A.; Chistov, R.; Markin, O.; Polikarpov, S.; Andreev, V.; Azarkin, M.; Dremin, I.; Kirakosyan, M.; Leonidov, A.; Terkulov, A.; Baskakov, A.; Belyaev, A.; Boos, E.; Ershov, A.; Gribushin, A.; Kaminskiy, A.; Kodolova, O.; Korotkikh, V.; Lokhtin, I.; Miagkov, I.; Obraztsov, S.; Petrushanko, S.; Savrin, V.; Snigirev, A.; Vardanyan, I.; Blinov, V.; Skovpen, Y.; Shtol, D.; Azhgirey, I.; Bayshev, I.; Bitioukov, S.; Elumakhov, D.; Kachanov, V.; Kalinin, A.; Konstantinov, D.; Krychkine, V.; Petrov, V.; Ryutin, R.; Sobol, A.; Troshin, S.; Tyurin, N.; Uzunian, A.; Volkov, A.; Adzic, P.; Cirkovic, P.; Devetak, D.; Dordevic, M.; Milosevic, J.; Rekovic, V.; Alcaraz Maestre, J.; Barrio Luna, M.; Calvo, E.; Cerrada, M.; Chamizo Llatas, M.; Colino, N.; De La Cruz, B.; Delgado Peris, A.; Escalante Del Valle, A.; Fernandez Bedoya, C.; Fernández Ramos, J. P.; Flix, J.; Fouz, M. C.; Garcia-Abia, P.; Gonzalez Lopez, O.; Goy Lopez, S.; Hernandez, J. M.; Josa, M. I.; Navarro De Martino, E.; Pérez-Calero Yzquierdo, A.; Puerta Pelayo, J.; Quintario Olmeda, A.; Redondo, I.; Romero, L.; Soares, M. S.; de Trocóniz, J. F.; Missiroli, M.; Moran, D.; Cuevas, J.; Fernandez Menendez, J.; Gonzalez Caballero, I.; González Fernández, J. R.; Palencia Cortezon, E.; Sanchez Cruz, S.; Suárez Andrés, I.; Vizan Garcia, J. M.; Cabrillo, I. J.; Calderon, A.; Castiñeiras De Saa, J. R.; Curras, E.; Fernandez, M.; Garcia-Ferrero, J.; Gomez, G.; Lopez Virto, A.; Marco, J.; Martinez Rivero, C.; Matorras, F.; Piedra Gomez, J.; Rodrigo, T.; Ruiz-Jimeno, A.; Scodellaro, L.; Trevisani, N.; Vila, I.; Vilar Cortabitarte, R.; Abbaneo, D.; Auffray, E.; Auzinger, G.; Bachtis, M.; Baillon, P.; Ball, A. 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A.; Buchanan, J.; Caillol, C.; Dasu, S.; Dodd, L.; Duric, S.; Gomber, B.; Grothe, M.; Herndon, M.; Hervé, A.; Klabbers, P.; Lanaro, A.; Levine, A.; Long, K.; Loveless, R.; Ojalvo, I.; Perry, T.; Pierro, G. A.; Polese, G.; Ruggles, T.; Savin, A.; Smith, N.; Smith, W. H.; Taylor, D.; Woods, N.; CMS Collaboration

2017-04-01

The relative modification of the prompt ψ (2 S ) and J /ψ yields from p p to PbPb collisions, at the center-of-mass energy of 5.02 TeV per nucleon pair, is presented. The analysis is based on p p and PbPb data samples collected by the CMS experiment at the LHC in 2015, corresponding to integrated luminosities of 28.0 pb-1 and 464 μ b-1 , respectively. The double ratio of measured yields of prompt charmonia reconstructed through their decays into muon pairs, (Nψ (2 S )/NJ /ψ)PbPb/(Nψ (2 S )/NJ /ψ)p p , is determined as a function of PbPb collision centrality and charmonium transverse momentum pT, in two kinematic intervals: |y | <1.6 covering 6.5

Morphological and acoustic characterization of Proceratophrys goyana (Lissamphibia: Anura: Odontophrynidae), with the description of a sympatric and related new species.

PubMed

Martins, Lucas Borges; Giaretta, Ariovaldo Antonio

2013-12-20

Proceratophrys goyana was until recently the only species of the genus described from central Brazil. In this paper we characterize the adult morphology and advertisement call of this species, based on data collected at its type-locality (Chapada dos Veadeiros, Goiás, Brazil). These new data allowed us to recognize a new species of Proceratophrys, sympatric to P. goyana, which is described herein. Proceratophrys goyana is mainly characterized by the male SVL = 38.8-46.5 mm; a well-developed and continuous pair of dorsal sagittal ridges; upper eyelids triangular; developed frontoparietal crests, delimiting a shallow depression between them; overall color pattern browned, with the symmetrical dorsal ridges bordered laterally by dark brown undulations. Proceratophrys rotundipalpebra sp. nov. is characterized by the male SVL = 30.4-39.3 mm; the pair of symmetrical dorsal ridges well-developed anteriorly and somewhat interrupted in the sacral region; upper eyelids short and rounded; frontoparietal crests not well-developed; overall color pattern stained by 3-4 tonalities of gray, without a clear background color. The advertisement calls of both species are emitted in a multi-note pattern, each note pulsed, the first and last notes differing from each other and from those amidst the call in temporal features. The description of this new species is another example of the underestimated diversity of Proceratophrys in the Cerrado of central Brazil. 

Fiber optic gap gauge

DOEpatents

Wood, Billy E [Livermore, CA; Groves, Scott E [Brentwood, CA; Larsen, Greg J [Brentwood, CA; Sanchez, Roberto J [Pleasanton, CA

2006-11-14

A lightweight, small size, high sensitivity gauge for indirectly measuring displacement or absolute gap width by measuring axial strain in an orthogonal direction to the displacement/gap width. The gap gauge includes a preferably titanium base having a central tension bar with springs connecting opposite ends of the tension bar to a pair of end connector bars, and an elongated bow spring connected to the end connector bars with a middle section bowed away from the base to define a gap. The bow spring is capable of producing an axial strain in the base proportional to a displacement of the middle section in a direction orthogonal to the base. And a strain sensor, such as a Fabry-Perot interferometer strain sensor, is connected to measure the axial strain in the base, so that the displacement of the middle section may be indirectly determined from the measurement of the axial strain in the base.

POST ASYMPTOTIC GIANT BRANCH BIPOLAR REFLECTION NEBULAE: RESULT OF DYNAMICAL EJECTION OR SELECTIVE ILLUMINATION?

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

Koning, N.; Kwok, Sun; Steffen, W., E-mail: nico.koning@ucalgary.ca, E-mail: sunkwok@hku.hk, E-mail: wsteffen@astrosen.unam.mx

2013-03-10

A model for post asymptotic giant branch bipolar reflection nebulae has been constructed based on a pair of evacuated cavities in a spherical dust envelope. Many of the observed features of bipolar nebulae, including filled bipolar lobes, an equatorial torus, searchlight beams, and a bright central light source, can be reproduced. The effects on orientation and dust densities are studied and comparisons with some observed examples are offered. We suggest that many observed properties of bipolar nebulae are the result of optical effects and any physical modeling of these nebulae has to take these factors into consideration.

N = 2 supersymmetry and Bailey pairs

NASA Astrophysics Data System (ADS)

Berkovich, Alexander; McCoy, Barry M.; Schilling, Anne

1996-02-01

We demonstrate that the Bailey pair formulation of Rogers-Ramanujan identities unifies the calculations of the characters of N = 1 and N = 2 supersymmetric conformal field theories with the counterpart theory with no supersymmetry. We illustrate this construction for the M(3,4) (Ising) model where the Bailey pairs have been given by Slater. We then present the general unitary case. We demonstrate that the model M( p,p + 1) is derived from M( p - 1, p) by a Bailey renormalization flow and conclude by obtaining the N = 1 model SM( p,p + 2) and the unitary N = 2 model with central charge c = 3(1 - 2/ p).

Pairing Symmetry Transitions in the Even-Denominator FQHE System

NASA Astrophysics Data System (ADS)

Nomura, Kentaro; Yoshioka, Daijiro

2001-12-01

Transitions from a paired quantum Hall state to another quantum Hall state in bilayer systems are discussed in the framework of the edge theory. Starting from the edge theory for the Haldane Rezayi state, it is shown that the charging effect of a bilayer system which breaks the SU(2) symmetry of the pseudospin shifts the central charge and the conformal dimensions of the fermionic fields which describe the pseudospin sector in the edge theory. This corresponds to the transition from the Haldane Rezayi state to Halperin's 331 state, or from a singlet d-wave to a triplet p-wave ABM type paired state in the composite fermion picture. Considering interlayer tunneling, the tunneling rate-capacitance phase diagram for the ν=5/2 paired bilayer system is discussed.

The magnetic toroidal sector: a broad-band electron-positron pair spectrometer

NASA Astrophysics Data System (ADS)

Hagmann, Siegbert; Hillenbrand, Pierre-Michel; Litvinov, Yuri; Spillmann, Uwe

2016-05-01

At the future relativistic storage-ring HESR at FAIR the study of electron-positron pairs from non-nuclear, atomic processes will be one of the goals of the experimental program with kinematically complete experiments focusing on momentum spectroscopy of coincident emission of electrons and positrons from free-free pairs and corresponding recoil ions. The underlying production mechanisms belong to central topics of QED in strong fields. We present first results on the electron-optical properties of a magnetic toroidal sector configuration enabling coincident detection of free-free electron-positron pairs; this spectrometer is suitable for implementation into a storage ring with a supersonic jet target and covering a wide range of lepton emission into the forward hemisphere. The simulation calculations are performed using the OPERA code.

Conditions for the successful integration of Human and Organizational Factors (HOF) in the nuclear safety analysis.

PubMed

Tosello, Michèle; Lévêque, Françoise; Dutillieu, Stéphanie; Hernandez, Guillaume; Vautier, Jean-François

2012-01-01

This communication presents some elements which come from the experience feedback at CEA about the conditions for the successful integration of HOF in the nuclear safety analysis. To point out some of these conditions, one of the concepts proposed by Edgar Morin to describe the functioning of "complex" systems: the dialogical principle has been used. The idea is to look for some dialogical pairs. The elements of this kind of pair are both complementary and antagonist to one another. Three dialogical pairs are presented in this communication. The first two pairs are related to the organization of the HOF network and the last one is related to the methods which are used to analyse the working situations. The three pairs are: specialist - non-specialist actors of the network, centralized - distributed human resources in the network and microscopic - macroscopic levels of HOF methods to analyse the working situations. To continuously improve these three dialogical pairs, it is important to keep the differences which exist between the two elements of a pair and to find and maintain a balance between the two elements of the pairs.

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

NASA Astrophysics Data System (ADS)

Yang, Bo; Rodgers, M. T.

2015-08-01

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

Estimating the color of maxillary central incisors based on age and gender

PubMed Central

Gozalo-Diaz, David; Johnston, William M.; Wee, Alvin G.

2008-01-01

Statement of problem There is no scientific information regarding the selection of the color of teeth for edentulous patients. Purpose The purpose of this study was to evaluate linear regression models that may be used to predict color parameters for central incisors of edentulous patients based on some characteristics of dentate subjects. Material and methods A spectroradiometer and an external light source were set in a noncontacting 45/0 degree (45-degree illumination and 0-degree observer) optical configuration to measure the color of subjects’ vital craniofacial structures (maxillary central incisor, attached gingiva, and facial skin). The subjects (n=120) were stratified into 5 age groups with 4 racial groups and balanced for gender. Linear first-order regression was used to determine the significant factors (α=.05) in the prediction model for each color direction of the color of the maxillary central incisor. Age, gender, and color of the other craniofacial structures were studied as potential predictors. Final predictions in each color direction were based only on the statistically significant factors, and then the color differences between observed and predicted CIELAB values for the central incisors were calculated and summarized. Results The statistically significant predictors of age and gender accounted for 36% of the total variability in L*. The statistically significant predictor of age accounted for 16% of the total variability in a*. The statistically significant predictors of age and gender accounted for 21% of the variability in b*. The mean ΔE (SD) between predicted and observed CIELAB values for the central incisor was 5.8 (3.2). Conclusions Age and gender were found to be statistically significant determinants in predicting the natural color of central incisors. Although the precision of these predictions was less than the median color difference found for all pairs of teeth studied, and may be considered an acceptable precision, further study is needed to reduce this precision to the limit of detection. Clinical Implications Age is highly correlated with the natural color of the central incisors. When age increases, the central incisor becomes darker, more reddish, and more yellow. Also, the women subjects in this study had lighter and less yellow central incisors than the men. PMID:18672125

Applied Meteorology Unit Quarterly Report, Second Quarter FY-13

NASA Technical Reports Server (NTRS)

Bauman, William; Crawford, Winifred; Watson, Leela; Shafer, Jaclyn; Huddleston, Lisa

2013-01-01

The AMU team worked on six tasks for their customers: (1) Ms. Crawford continued work on the objective lightning forecast task for airports in east-central Florida, and began work on developing a dual-Doppler analysis with local Doppler radars, (2) Ms. Shafer continued work for Vandenberg Air Force Base on an automated tool to relate pressure gradients to peak winds, (3) Dr. Huddleston continued work to develop a lightning timing forecast tool for the Kennedy Space Center/Cape Canaveral Air Force Station area, (4) Dr. Bauman continued work on a severe weather forecast tool focused on east-central Florida, (5) Mr. Decker began developing a wind pairs database for the Launch Services Program to use when evaluating upper-level winds for launch vehicles, and (6) Dr. Watson began work to assimilate observational data into the high-resolution model configurations, she created for Wallops Flight Facility and the Eastern Range.

Optogenetic Central Amygdala Stimulation Intensifies and Narrows Motivation for Cocaine.

PubMed

Warlow, Shelley M; Robinson, Mike J F; Berridge, Kent C

2017-08-30

Addiction is often characterized by intense motivation for a drug, which may be narrowly focused at the expense of other rewards. Here, we examined the role of amygdala-related circuitry in the amplification and narrowing of motivation focus for intravenous cocaine. We paired optogenetic channelrhodopsin (ChR2) stimulation in either central nucleus of amygdala (CeA) or basolateral amygdala (BLA) of female rats with one particular nose-poke porthole option for earning cocaine infusions (0.3 mg/kg, i.v.). A second alternative porthole earned identical cocaine but without ChR2 stimulation. Consequently, CeA rats quickly came to pursue their CeA ChR2-paired cocaine option intensely and exclusively, elevating cocaine intake while ignoring their alternative cocaine alone option. By comparison, BLA ChR2 pairing failed to enhance cocaine motivation. CeA rats also emitted consummatory bites toward their laser-paired porthole, suggesting that higher incentive salience made that cue more attractive. A separate progressive ratio test of incentive motivation confirmed that CeA ChR2 amplified rats' motivation, raising their breakpoint effort price for cocaine by 10-fold. However, CeA ChR2 laser on its own lacked any reinforcement value: laser by itself was never self-stimulated, not even by the same rats in which it amplified motivation for cocaine. Conversely, CeA inhibition by muscimol/baclofen microinjections prevented acquisition of cocaine self-administration and laser preference, whereas CeA inhibition by optogenetic halorhodopsin suppressed cocaine intake, indicating that CeA circuitry is needed for ordinary cocaine motivation. We conclude that CeA ChR2 excitation paired with a cocaine option specifically focuses and amplifies motivation to produce intense pursuit and consumption focused on that single target. SIGNIFICANCE STATEMENT In addiction, intense incentive motivation often becomes narrowly focused on a particular drug of abuse. Here we show that pairing central nucleus of amygdala (CeA) optogenetic stimulation with one option for earning intravenous cocaine makes that option almost the exclusive focus of intense pursuit and consumption. CeA stimulation also elevated the effort cost rats were willing to pay for cocaine and made associated cues become intensely attractive. However, we also show that CeA laser had no reinforcing properties at all when given alone for the same rats. Therefore, CeA laser pairing makes its associated cocaine option and cues become powerfully attractive in a nearly addictive fashion. Copyright © 2017 the authors 0270-6474/17/378330-19$15.00/0.

Optogenetic Central Amygdala Stimulation Intensifies and Narrows Motivation for Cocaine

PubMed Central

2017-01-01

Addiction is often characterized by intense motivation for a drug, which may be narrowly focused at the expense of other rewards. Here, we examined the role of amygdala-related circuitry in the amplification and narrowing of motivation focus for intravenous cocaine. We paired optogenetic channelrhodopsin (ChR2) stimulation in either central nucleus of amygdala (CeA) or basolateral amygdala (BLA) of female rats with one particular nose-poke porthole option for earning cocaine infusions (0.3 mg/kg, i.v.). A second alternative porthole earned identical cocaine but without ChR2 stimulation. Consequently, CeA rats quickly came to pursue their CeA ChR2-paired cocaine option intensely and exclusively, elevating cocaine intake while ignoring their alternative cocaine alone option. By comparison, BLA ChR2 pairing failed to enhance cocaine motivation. CeA rats also emitted consummatory bites toward their laser-paired porthole, suggesting that higher incentive salience made that cue more attractive. A separate progressive ratio test of incentive motivation confirmed that CeA ChR2 amplified rats' motivation, raising their breakpoint effort price for cocaine by 10-fold. However, CeA ChR2 laser on its own lacked any reinforcement value: laser by itself was never self-stimulated, not even by the same rats in which it amplified motivation for cocaine. Conversely, CeA inhibition by muscimol/baclofen microinjections prevented acquisition of cocaine self-administration and laser preference, whereas CeA inhibition by optogenetic halorhodopsin suppressed cocaine intake, indicating that CeA circuitry is needed for ordinary cocaine motivation. We conclude that CeA ChR2 excitation paired with a cocaine option specifically focuses and amplifies motivation to produce intense pursuit and consumption focused on that single target. SIGNIFICANCE STATEMENT In addiction, intense incentive motivation often becomes narrowly focused on a particular drug of abuse. Here we show that pairing central nucleus of amygdala (CeA) optogenetic stimulation with one option for earning intravenous cocaine makes that option almost the exclusive focus of intense pursuit and consumption. CeA stimulation also elevated the effort cost rats were willing to pay for cocaine and made associated cues become intensely attractive. However, we also show that CeA laser had no reinforcing properties at all when given alone for the same rats. Therefore, CeA laser pairing makes its associated cocaine option and cues become powerfully attractive in a nearly addictive fashion. PMID:28751460

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

PubMed

Paukku, Y; Hill, G

2011-05-12

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

Exclusive Central pi+pi- production in CDF

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

Albrow, Michael; Swiech, Artur; Zurek, Maria

2013-10-14

Using the Collider Detector at Fermilab, CDF, we have measured exclusive pi+pi- production at sqrt(s) = 900 GeV and 1960 GeV. The pi+pi- pair is central, |y| < 1.0, and there are no other particles detected in |eta| < 5.9. We discuss the mass spectrum, showing f0(980) and f2(1270) resonances, s-dependence, pT-dependence, and angular distributions.

Applications of CRISPR/Cas9 in the Mammalian Central Nervous System



PubMed Central

Savell, Katherine E.; Day, Jeremy J.

2017-01-01

Within the central nervous system, gene regulatory mechanisms are crucial regulators of cellular development and function, and dysregulation of these systems is commonly observed in major neuropsychiatric and neurological disorders. However, due to a lack of tools to specifically modulate the genome and epigenome in the central nervous system, many molecular and genetic mechanisms underlying cognitive function and behavior are still unknown. Although genome editing tools have been around for decades, the recent emergence of inexpensive, straightforward, and widely accessible CRISPR/Cas9 systems has led to a revolution in gene editing. The development of the catalytically dead Cas9 (dCas9) expanded this flexibility even further by acting as an anchoring system for fused effector proteins, structural scaffolds, and RNAs. Together, these advances have enabled robust, modular approaches for specific targeting and modification of the local chromatin environment at a single gene. This review highlights these advancements and how the combination of powerful modulatory tools paired with the versatility of CRISPR-Cas9-based systems offer great potential for understanding the underlying genetic and epigenetic contributions of neuronal function, behavior, and neurobiological diseases. PMID:29259522

Contribution of inter-muscular synchronization in the modulation of tremor intensity in Parkinson's disease.

PubMed

He, Xin; Hao, Man-Zhao; Wei, Ming; Xiao, Qin; Lan, Ning

2015-12-01

Involuntary central oscillations at single and double tremor frequencies drive the peripheral neuromechanical system of muscles and joints to cause tremor in Parkinson's disease (PD). The central signal of double tremor frequency was found to correlate more directly to individual muscle EMGs (Timmermann et al. 2003). This study is aimed at investigating what central components of oscillation contribute to inter-muscular synchronization in a group of upper extremity muscles during tremor in PD patients. 11 idiopathic, tremor dominant PD subjects participated in this study. Joint kinematics during tremor in the upper extremity was recorded along with EMGs of six upper arm muscles using a novel experimental apparatus. The apparatus provided support for the upper extremity on a horizontal surface with reduced friction, so that resting tremor in the arm can be recorded with a MotionMonitor II system. In each subject, the frequencies of rhythmic firings in upper arm muscles were determined using spectral analysis. Paired and pool-averaged coherence analyses of EMGs for the group of muscles were performed to correlate the level of inter-muscular synchronization to tremor amplitudes at shoulder and elbow. The phase shift between synchronized antagonistic muscle pairs was calculated to aid coherence analysis in the muscle pool. Recorded EMG revealed that rhythmic firings were present in most recorded muscles, which were either synchronized to form phase-locked bursting cycles at a subject specific frequency, or unsynchronized with a random phase distribution. Paired coherence showed a stronger synchronization among a subset of recorded arm muscles at tremor frequency than that at double tremor frequency. Furthermore, the number of synchronized muscles in the arm was positively correlated to tremor amplitudes at elbow and shoulder. Pool-averaged coherence at tremor frequency also showed a better correlation with the amplitude of resting tremor than that of double tremor frequency, indicating that the neuromechanical coupling in peripheral neuromuscular system was stronger at tremor frequency. Both paired and pool-averaged coherences are more consistent indexes to correlate to tremor intensity in a group of upper extremity muscles of PD patients. The central drive at tremor frequency contributes mainly to synchronize peripheral muscles in the modulation of tremor intensity.

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

PubMed Central

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

2011-01-01

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

Modeling the secular evolution of migrating planet pairs

NASA Astrophysics Data System (ADS)

Michtchenko, T. A.; Rodríguez, A.

2011-10-01

The secular regime of motion of multi-planetary systems is universal; in contrast with the 'accidental' resonant motion, characteristic only for specific configurations of the planets, secular motion is present everywhere in phase space, even inside the resonant region. The secular behavior of a pair of planets evolving under dissipative forces is the principal subject of this study, particularly, the case when the dissipative forces affect the planetary semi-major axes and the planets move inward/outward the central star, the process known as planet migration. Based on the fundamental concepts of conservative and dissipative dynamics of the three-body problem, we develop a qualitative model of the secular evolution of the migrating planetary pair. Our approach is based on analysis of the energy and the orbital angular momentum exchange between the two-planet system and an external medium; thus no specific kind of dissipative forces is invoked. We show that, under assumption that dissipation is weak and slow, the evolutionary routes of the migrating planets are traced by the Mode I and Mode II stationary solutions of the conservative secular problem. The ultimate convergence and the evolution of the system along one of these secular modes of motion is determined uniquely by the condition that the dissipation rate is sufficiently smaller than the proper secular frequency of the system. We show that it is possible to reassemble the starting configurations and migration history of the systems on the basis of their final states and consequently to constrain the parameters of the physical processes involved.

Manipulation of the oxytocin system alters social behavior and attraction in pair-bonding primates, Callithrix penicillata

PubMed Central

Smith, Adam S.; Ågmo, Anders; Birnie, Andrew K.; French, Jeffrey A.

2010-01-01

The establishment and maintenance of stable, long-term male-female relationships, or pair bonds, are marked by high levels of mutual attraction, selective preference for the partner, and high rates of sociosexual behavior. Central oxytocin (OT) affects social preference and partner-directed social behavior in rodents, but the role of this neuropeptide has yet to be studied in heterosexual primate relationships. The present study evaluated whether the OT system plays a role in the dynamics of social behavior and partner preference during the first three weeks of cohabitation in male and female marmosets, Callithrix penicillata. OT activity was stimulated by intranasal administration of OT, and inhibited by oral administration of a non-peptide OT-receptor antagonist (L-368,899; Merck). Social behavior throughout the pairing varied as a function of OT treatment. Compared to controls, marmosets initiated huddling with their social partner more often after OT treatments but reduced proximity and huddling after OT antagonist treatments. OT antagonist treatment also eliminated food sharing between partners. During the 24-h preference test, all marmosets interacted more with an opposite-sex stranger than with the partner. By the third-week preference test, marmosets interacted with the partner and stranger equally with the exception that intranasal-OT treatments facilitated initial partner-seeking behavior over initial contact with the stranger. Our findings demonstrate that pharmacological manipulations of OT activity alter partner-directed social behavior during pair interactions, suggesting that central OT may facilitate the process of pair-bond formation and social relationships in marmoset monkeys. PMID:20025881

Manipulation of the oxytocin system alters social behavior and attraction in pair-bonding primates, Callithrix penicillata.

PubMed

Smith, Adam S; Agmo, Anders; Birnie, Andrew K; French, Jeffrey A

2010-02-01

The establishment and maintenance of stable, long-term male-female relationships, or pair-bonds, are marked by high levels of mutual attraction, selective preference for the partner, and high rates of sociosexual behavior. Central oxytocin (OT) affects social preference and partner-directed social behavior in rodents, but the role of this neuropeptide has yet to be studied in heterosexual primate relationships. The present study evaluated whether the OT system plays a role in the dynamics of social behavior and partner preference during the first 3 weeks of cohabitation in male and female marmosets, Callithrix penicillata. OT activity was stimulated by intranasal administration of OT, and inhibited by oral administration of a non-peptide OT-receptor antagonist (L-368,899; Merck). Social behavior throughout the pairing varied as a function of OT treatment. Compared to controls, marmosets initiated huddling with their social partner more often after OT treatments but reduced proximity and huddling after OT antagonist treatments. OT antagonist treatment also eliminated food sharing between partners. During the 24-h preference test, all marmosets interacted more with an opposite-sex stranger than with the partner. By the third-week preference test, marmosets interacted with the partner and stranger equally with the exception that intranasal-OT treatments facilitated initial partner-seeking behavior over initial contact with the stranger. Our findings demonstrate that pharmacological manipulations of OT activity alter partner-directed social behavior during pair interactions, suggesting that central OT may facilitate the process of pair-bond formation and social relationships in marmoset monkeys. Published by Elsevier Inc.

Kinetic measurement of 2-aminopurine X cytosine and 2-aminopurine X thymine base pairs as a test of DNA polymerase fidelity mechanisms.

PubMed Central

Watanabe, S M; Goodman, M F

1982-01-01

Enzyme kinetic measurements are presented showing that Km rather than maximum velocity (Vmax) discrimination governs the frequency of forming 2-aminopurine X cytosine base mispairs by DNA polymerase alpha. An in vitro system is used in which incorporation of dTMP or dCMP occurs opposite a template 2-aminopurine, and values for Km and Vmax are obtained. Results from a previous study in which dTTP and dCTP were competing simultaneously for insertion opposite 2-aminopurine indicated that dTMP is inserted 22 times more frequently than dCMP. We now report that the ratio of Km values KCm/KTm = 25 +/- 6, which agrees quantitatively with the dTMP/dCMP incorporation ratio obtained previously. We also report that VCmax is indistinguishable from VTmax. These Km and Vmax data are consistent with predictions from a model, the Km discrimination model, in which replication fidelity is determined by free energy differences between matched and mismatched base pairs. Central to this model is the prediction that the ratio of Km values for insertion of correct and incorrect nucleotides specifies the insertion fidelity, and the maximum velocities of insertion are the same for both nucleotides. PMID:6959128

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

PubMed Central

Seelam, Preethi P.; Sharma, Purshotam

2017-01-01

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

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

PubMed

Ito, Yuko; Sone, Yumiko; Mizutani, Takaharu

2004-03-01

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

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

NASA Astrophysics Data System (ADS)

(O' Lee, Dominic J.

2018-02-01

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

SU-E-T-01: 2-D Characterization of DLG Among All MLC Leaf Pairs

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

Kumaraswamy, L; Xu, Z; Podgorsak, M

Purpose: The aim of this study is to evaluate the variation of dosimetric leaf-gap (DLG) along the travel path of each MLC leaf pair. This study evaluates whether the spatial variations in DLG could cause dose differences between TPS-calculated and measured dose. Methods: The 6MV DLG values were measured for all leaf pairs in the direction of leaf motion using a 2-D diode array and 0.6cc ion chamber. These measurements were performed on two Varian Linacs, employing the Millennium 120-leaf MLC and a 2-D-DLG variation map was created via in-house software. Several test plans were created with sweeping MLC fieldsmore » using constant gaps from 2mm to 10mm and corrected for 2-D variation utilizing in-house software. Measurements were performed utilizing the MapCHECK at 5.0cm depth for plans with and without the 2-D DLG correction and compared to the TPS calculated dose via gamma analysis (3%/3mm). Results: The measured DLGs for the middle 40 MLC leaf pairs (0.5cm width) were very similar along the central superior-inferior axis, with maximum variation of 0.2mm. The outer 20 MLC leaf pairs (1.0cm width) have DLG values from 0.32mm (mean) to 0.65mm (maximum) lower than the central leaf-pair, depending on off-axis distance. Gamma pass rates for the 2mm, 4mm, and 6mm sweep plans increased by 23.2%, 28.7%, and 26.0% respectively using the 2-D-DLG correction. The most improved dose points occur in areas modulated by the 1.0cm leaf-pairs. The gamma pass rate for the 10mm sweep plan increased by only 7.7%, indicating that the 2D variation becomes less significant for dynamic plans with larger MLC gaps. Conclusion: Fluences residing significantly off-axis with narrow sweeping gaps may exhibit significant variations from planned dose due to large differences between the true DLG exhibited by the 1.0cm leaf-pairs versus the constant DLG value utilized by the TPS for dose calculation.« less

Territorial behavior, pesticides, and the population ecology of red-shouldered hawks in central Maryland, 1943-1971

USGS Publications Warehouse

Henny, C.J.; Schmid, F.C.; Martin, E.M.; Hood, L.L.

1973-01-01

A breeding population of red-shouldered hawks (Buteo lineatus) along the Patuxent River in central Maryland was studied during the interval 1943-71. Numbers of breeding pairs remained unchanged or increased on the PWRC (Patuxent Wildlife Research Center) and an adjoining area where habitat was not altered. A reduction in breeding pairs occurred on the third study area where large portions of the habitat had been destroyed. Basic information on 74 nests was obtained and the annual number of breeding pairs on the PWRC ranged from a low of four to a high of nine during the study. Nesting success of this highly territorial species decreased significantly as the distance between adjacent nest sites decreased (Errington's principle of inversity). Since 1960, the recruitment rate during high density years was 1.34 young fledged per pair as opposed to 1.95 during optimum (1943 and 1947 levels) density years. The 1.95 figure compared favorably with the estimated recruitment rate necessary for maintaining a stable population and with recruitment rates observed in other locations prior to the modern pesticide era. As the observed recruitment rate during the 4 years of optimum density was believed adequate, it is doubtful that the relatively low pesticide levels in the eggs had a detrimental effect on the reproductive performance of the population.

Phenotypic covariance at species’ borders

PubMed Central

2013-01-01

Background Understanding the evolution of species limits is important in ecology, evolution, and conservation biology. Despite its likely importance in the evolution of these limits, little is known about phenotypic covariance in geographically marginal populations, and the degree to which it constrains, or facilitates, responses to selection. We investigated phenotypic covariance in morphological traits at species’ borders by comparing phenotypic covariance matrices (P), including the degree of shared structure, the distribution of strengths of pair-wise correlations between traits, the degree of morphological integration of traits, and the ranks of matricies, between central and marginal populations of three species-pairs of coral reef fishes. Results Greater structural differences in P were observed between populations close to range margins and conspecific populations toward range centres, than between pairs of conspecific populations that were both more centrally located within their ranges. Approximately 80% of all pair-wise trait correlations within populations were greater in the north, but these differences were unrelated to the position of the sampled population with respect to the geographic range of the species. Conclusions Neither the degree of morphological integration, nor ranks of P, indicated greater evolutionary constraint at range edges. Characteristics of P observed here provide no support for constraint contributing to the formation of these species’ borders, but may instead reflect structural change in P caused by selection or drift, and their potential to evolve in the future. PMID:23714580

Optogenetic Excitation of Central Amygdala Amplifies and Narrows Incentive Motivation to Pursue One Reward Above Another

PubMed Central

Warlow, Shelley M.; Berridge, Kent C.

2014-01-01

Choosing one reward above another is important for achieving adaptive life goals. Yet hijacked into excessive intensity in disorders such as addiction, single-minded pursuit becomes maladaptive. Here, we report that optogenetic channelrhodopsin stimulation of neurons in central nucleus of amygdala (CeA), paired with earning a particular sucrose reward in rats, amplified and narrowed incentive motivation to that single reward target. Therefore, CeA rats chose and intensely pursued only the laser-paired sucrose reward while ignoring an equally good sucrose alternative. In contrast, reward-paired stimulation of basolateral amygdala did not hijack choice. In a separate measure of incentive motivation, CeA stimulation also increased the progressive ratio breakpoint or level of effort exerted to obtain sucrose reward. However, CeA stimulation by itself failed to support behavioral self-stimulation in the absence of any paired external food reward, suggesting that CeA photo-excitation specifically transformed the value of its external reward (rather than adding an internal reinforcement state). Nor did CeA stimulation by itself induce any aversive state that motivated escape. Finally, CeA stimulation also failed to enhance ‘liking’ reactions elicited by sucrose taste and did not simply increase the general motivation to eat. This pattern suggests that CeA photo-excitation specifically enhances and narrows incentive motivation to pursue an associated external reward at the expense of another comparable reward. PMID:25505310

Phenotypic covariance at species' borders.

PubMed

Caley, M Julian; Cripps, Edward; Game, Edward T

2013-05-28

Understanding the evolution of species limits is important in ecology, evolution, and conservation biology. Despite its likely importance in the evolution of these limits, little is known about phenotypic covariance in geographically marginal populations, and the degree to which it constrains, or facilitates, responses to selection. We investigated phenotypic covariance in morphological traits at species' borders by comparing phenotypic covariance matrices (P), including the degree of shared structure, the distribution of strengths of pair-wise correlations between traits, the degree of morphological integration of traits, and the ranks of matricies, between central and marginal populations of three species-pairs of coral reef fishes. Greater structural differences in P were observed between populations close to range margins and conspecific populations toward range centres, than between pairs of conspecific populations that were both more centrally located within their ranges. Approximately 80% of all pair-wise trait correlations within populations were greater in the north, but these differences were unrelated to the position of the sampled population with respect to the geographic range of the species. Neither the degree of morphological integration, nor ranks of P, indicated greater evolutionary constraint at range edges. Characteristics of P observed here provide no support for constraint contributing to the formation of these species' borders, but may instead reflect structural change in P caused by selection or drift, and their potential to evolve in the future.

Vascular development in the retina and inner ear: control by Norrin and Frizzled-4, a high-affinity ligand-receptor pair.

PubMed

Xu, Qiang; Wang, Yanshu; Dabdoub, Alain; Smallwood, Philip M; Williams, John; Woods, Chad; Kelley, Matthew W; Jiang, Li; Tasman, William; Zhang, Kang; Nathans, Jeremy

2004-03-19

Incomplete retinal vascularization occurs in both Norrie disease and familial exudative vitreoretinopathy (FEVR). Norrin, the protein product of the Norrie disease gene, is a secreted protein of unknown biochemical function. One form of FEVR is caused by defects in Frizzled-4 (Fz4), a presumptive Wnt receptor. We show here that Norrin and Fz4 function as a ligand-receptor pair based on (1) the similarity in vascular phenotypes caused by Norrin and Fz4 mutations in humans and mice, (2) the specificity and high affinity of Norrin-Fz4 binding, (3) the high efficiency with which Norrin induces Fz4- and Lrp-dependent activation of the classical Wnt pathway, and (4) the signaling defects displayed by disease-associated variants of Norrin and Fz4. These data define a Norrin-Fz4 signaling system that plays a central role in vascular development in the eye and ear, and they indicate that ligands unrelated to Wnts can act through Fz receptors.

Enhanced sampling simulations of DNA step parameters.

PubMed

Karolak, Aleksandra; van der Vaart, Arjan

2014-12-15

A novel approach for the selection of step parameters as reaction coordinates in enhanced sampling simulations of DNA is presented. The method uses three atoms per base and does not require coordinate overlays or idealized base pairs. This allowed for a highly efficient implementation of the calculation of all step parameters and their Cartesian derivatives in molecular dynamics simulations. Good correlation between the calculated and actual twist, roll, tilt, shift, and slide parameters is obtained, while the correlation with rise is modest. The method is illustrated by its application to the methylated and unmethylated 5'-CATGTGACGTCACATG-3' double stranded DNA sequence. One-dimensional umbrella simulations indicate that the flexibility of the central CG step is only marginally affected by methylation. © 2014 Wiley Periodicals, Inc.

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

PubMed

Wilcox, Jennifer L; Bevilacqua, Philip C

2013-10-22

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

Interobserver concordance of assessments of dysplasia and blast counts for the diagnosis of patients with cytopenia: From the Japanese central review study.

PubMed

Matsuda, Akira; Kawabata, Hiroshi; Tohyama, Kaoru; Maeda, Tomoya; Araseki, Kayano; Hata, Tomoko; Suzuki, Takahiro; Kayano, Hidekazu; Shimbo, Kei; Usuki, Kensuke; Chiba, Shigeru; Ishikawa, Takayuki; Arima, Nobuyoshi; Nohgawa, Masaharu; Ohta, Akiko; Miyazaki, Yasushi; Nakao, Sinnji; Ozawa, Keiya; Arai, Shunya; Kurokawa, Mineo; Mitani, Kinuko; Takaori-Kondo, Akifumi

2018-06-07

The diagnosis of myelodysplastic syndromes (MDS) is based on morphology and cytogenetics. However, limited information is currently available on the interobserver concordance of the assessment of dysplastic lineages (<10% or ≥10% in bone marrow (BM)). The revised International Prognostic Scoring System (IPSS-R) described a new threshold (2%) for BM blasts. However, the interobserver concordance of the categories (0-≤2% and >2-<5%) has limited data. The purpose of the present study was to investigate the assessment of dysplastic lineages and IPSS-R reproducibility. Our study was divided into two Steps. In each Step, the microscopic examinations were performed separately by two morphologists. Regarding the category of BM blasts ≤2% and >2-<5%, interobserver agreement was more than 'moderate' in all pairs (kappa test: 0.43-0.90). Regarding dysgranulopoiesis (dysG) and dyserythropoiesis (dysE) in BM, interobserver agreement was more than 'moderate' in all pairs (kappa test, dysG: 0.45-0.96, dysE: 0.45-0.81). Regarding the category of dysmegakaryopoiesis (dysMgk) in BM, interobserver agreement was more than moderate in 4 out of 5 pairs (kappa test: 0.58-1.00), and was fair for one pair (kappa test: 0.37). We consider that high interobserver concordance may be possible for the BM blast cell count (≤2% or >2-<5%) and dysplasia (<10% or ≥10%) of each lineage. Copyright © 2018 Elsevier Ltd. All rights reserved.

Transferability of antibody pairs from ELISA to fiber optic surface plasmon resonance for infliximab detection

NASA Astrophysics Data System (ADS)

Van Stappen, Thomas; Lu, Jiadi; Bloemen, Maarten; Geukens, Nick; Spasic, Dragana; Delport, Filip; Verbiest, Thierry; Lammertyn, Jeroen; Gils, Ann

2015-03-01

Tumor necrosis factor (TNF)-alpha is a pleiotropic cytokine up-regulated in inflammatory bowel disease, rheumatoid arthritis and psoriasis. The introduction of anti-TNF drugs such as infliximab has revolutionized the treatment of these diseases. Recently, therapeutic drug monitoring (TDM) of infliximab has been introduced in clinical decision making to increase cost-efficiency. Nowadays, TDM is performed using radio-immunoassays, homogeneous mobility shift assays or ELISA. Unfortunately, these assays do not allow for in situ treatment optimization, because of the required sample transportation to centralized laboratories and the subsequent assay execution time. In this perspective, we evaluated the potential of fiber optic-surface plasmon resonance (FO-SPR). To achieve this goal, a panel of 55 monoclonal anti-infliximab antibodies (MA-IFX) was developed and characterized in-house, leading to the identification of nine different clusters. Based on this high diversity, 22 antibody pairs were selected and tested for their reactivity towards IFX, using one MA-IFX as capture and one MA-IFX for detection, in a sandwich type ELISA and FO-SPR. This study showed that the reactivity towards IFX of each antibody pair in ELISA is highly similar to its reactivity on FO-SPR, indicating that antibody pairs are easily transferable between both platforms. Given the fact that FO-SPR shows the potential for miniaturization and fast assay time, it can be considered a highly promising platform for on-site infliximab monitoring.

Hayward Fault, California Interferogram

NASA Image and Video Library

2000-08-17

This image of California Hayward fault is an interferogram created using a pair of images taken by ESA ERS-1 and ERS-2 in June 1992 and September 1997 over the central San Francisco Bay in California.

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

NASA Technical Reports Server (NTRS)

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

2000-01-01

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

Polyalanine expansion and frameshift mutations of the paired-like homeobox gene PHOX2B in congenital central hypoventilation syndrome.

PubMed

Amiel, Jeanne; Laudier, Béatrice; Attié-Bitach, Tania; Trang, Ha; de Pontual, Loïc; Gener, Blanca; Trochet, Delphine; Etchevers, Heather; Ray, Pierre; Simonneau, Michel; Vekemans, Michel; Munnich, Arnold; Gaultier, Claude; Lyonnet, Stanislas

2003-04-01

Congenital central hypoventilation syndrome (CCHS or Ondine's curse; OMIM 209880) is a life-threatening disorder involving an impaired ventilatory response to hypercarbia and hypoxemia. This core phenotype is associated with lower-penetrance anomalies of the autonomic nervous system (ANS) including Hirschsprung disease and tumors of neural-crest derivatives such as ganglioneuromas and neuroblastomas. In mice, the development of ANS reflex circuits is dependent on the paired-like homeobox gene Phox2b. Thus, we regarded its human ortholog, PHOX2B, as a candidate gene in CCHS. We found heterozygous de novo mutations in PHOX2B in 18 of 29 individuals with CCHS. Most mutations consisted of 5-9 alanine expansions within a 20-residue polyalanine tract probably resulting from non-homologous recombination. We show that PHOX2B is expressed in both the central and the peripheral ANS during human embryonic development. Our data support an essential role of PHOX2B in the normal patterning of the autonomous ventilation system and, more generally, of the ANS in humans.

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

PubMed Central

2017-01-01

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

Variable soft X-ray excesses in active galactic nuclei from nonthermal electron-positron pair cascades

NASA Technical Reports Server (NTRS)

Zdziarski, Andrzej A.; Coppi, Paolo S.

1991-01-01

In the present study of the formation of steep soft X-ray excesses that are superposed on flatter, hard X-ray power-law spectra in nonthermal electron-positron pair cascade sources, the soft excess in pair-cascade AGN models appears as a steep power law superposed on the tail of the UV bump and the flat nonthermal (hard X-ray) power law. The model-parameter space in which an excess in soft X-rays is visible is ascertained, and the time-variability of soft excesses in pair cascade models is examined. It is established that the parameter space in which soft excesses appear encompasses the range of preferred input parameters for a recently development Compton reflection model of UV and X-ray emission from the central engine of an AGN.

Transverse momentum and rapidity dependence of Hanbury-Brown Twiss correlations in Au+Au collisions at sNN= 62.4 and 200 GeV

NASA Astrophysics Data System (ADS)

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

2006-03-01

Two-particle correlations of identical charged pion pairs from Au+Au collisions at sNN=62.4 and 200 GeV were measured by the PHOBOS experiment at BNL Relativistic Heavy Ion Collider (RHIC). Data for the 15% most central events were analyzed with Bertsch-Pratt and Yano-Koonin-Podgoretskii parametrizations using pairs with rapidities of 0.4

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

PubMed

Shankar, Akshaya; Jagota, Anand; Mittal, Jeetain

2012-10-11

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

Study of lubricant circulation in HVAC systems. Volume 1: Description of technical effort and results; Final technical report, March 1995--April 1996

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

Biancardi, F.R.; Michels, H.H.; Sienel, T.H.

1996-10-01

The purpose of this program was to conduct experimental and analytical efforts to determine lubricant circulation characteristics of new HFC/POE pairs and HFC/mineral oil pairs in a representative central residential HVAC system and to compare their behavior with the traditional HCFC-22/mineral oil (refrigerant/lubricant) pair. A dynamic test facility was designed and built to conduct the experimental efforts. This facility provided a unique capability to visually and physically measure oil circulation rates, on-line, in operating systems. A unique on-line ultraviolet-based measurement device was used to obtain detailed data on the rate and level of lubricant oil circulated within the operating heatmore » pump system. The experimental and analytical data developed during the program are presented as a function of vapor velocity, refrigerant/lubricant viscosity, system features and equipment. Both visual observations and instrumentation were used to understand ``worst case`` oil circulation situations. This report is presented in two volumes. Volume 1 contains a complete description of the program scope, objective, test results summary, conclusions, description of test facility and recommendations for future effort. Volume 2 contains all of the program test data essentially as taken from the laboratory dynamic test facility during the sequence of runs.« less

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

NASA Technical Reports Server (NTRS)

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

1993-01-01

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

From bare to renormalized order parameter in gauge space: Structure and reactions

NASA Astrophysics Data System (ADS)

Potel, G.; Idini, A.; Barranco, F.; Vigezzi, E.; Broglia, R. A.

2017-09-01

It is not physically obvious why one can calculate with similar accuracy, as compared to the experimental data, the absolute cross section associated with two-nucleon transfer processes between members of pairing rotational bands, making use of simple BCS (constant matrix elements) or of many-body [Nambu-Gorkov (NG), nuclear field theory (NFT)] spectroscopic amplitudes. Restoration of spontaneous symmetry breaking and associated emergent generalized rigidity in gauge space provides the answer and points to a new emergence: A physical sum rule resulting from the intertwining of structure and reaction processes, closely connected with the central role induced pairing interaction plays in structure, together with the fact that successive transfer dominates Cooper pair tunneling.

Stereo Cameras for Clouds (STEREOCAM) Instrument Handbook

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

Romps, David; Oktem, Rusen

2017-10-31

The three pairs of stereo camera setups aim to provide synchronized and stereo calibrated time series of images that can be used for 3D cloud mask reconstruction. Each camera pair is positioned at approximately 120 degrees from the other pair, with a 17o-19o pitch angle from the ground, and at 5-6 km distance from the U.S. Department of Energy (DOE) Central Facility at the Atmospheric Radiation Measurement (ARM) Climate Research Facility Southern Great Plains (SGP) observatory to cover the region from northeast, northwest, and southern views. Images from both cameras of the same stereo setup can be paired together tomore » obtain 3D reconstruction by triangulation. 3D reconstructions from the ring of three stereo pairs can be combined together to generate a 3D mask from surrounding views. This handbook delivers all stereo reconstruction parameters of the cameras necessary to make 3D reconstructions from the stereo camera images.« less

In silico search for functionally similar proteins involved in meiosis and recombination in evolutionarily distant organisms.

PubMed

Bogdanov, Yuri F; Dadashev, Sergei Y; Grishaeva, Tatiana M

2003-01-01

Evolutionarily distant organisms have not only orthologs, but also nonhomologous proteins that build functionally similar subcellular structures. For instance, this is true with protein components of the synaptonemal complex (SC), a universal ultrastructure that ensures the successful pairing and recombination of homologous chromosomes during meiosis. We aimed at developing a method to search databases for genes that code for such nonhomologous but functionally analogous proteins. Advantage was taken of the ultrastructural parameters of SC and the conformation of SC proteins responsible for these. Proteins involved in SC central space are known to be similar in secondary structure. Using published data, we found a highly significant correlation between the width of the SC central space and the length of rod-shaped central domain of mammalian and yeast intermediate proteins forming transversal filaments in the SC central space. Basing on this, we suggested a method for searching genome databases of distant organisms for genes whose virtual proteins meet the above correlation requirement. Our recent finding of the Drosophila melanogaster CG17604 gene coding for synaptonemal complex transversal filament protein received experimental support from another lab. With the same strategy, we showed that the Arabidopsis thaliana and Caenorhabditis elegans genomes contain unique genes coding for such proteins.

Flow paths in the Edwards aquifer, northern Medina and northeastern Uvalde counties, Texas, based on hydrologic identification and geochemical characterization and simulation

USGS Publications Warehouse

Clark, Allan K.; Journey, Celeste A.

2006-01-01

The U.S. Geological Survey, in cooperation with the San Antonio Water System, conducted a 4-year study during 2001– 04 to identify major ground-water flow paths in the Edwards aquifer in northern Medina and northeastern Uvalde Counties, Texas. The study involved use of geologic structure, surfacewater and ground-water data, and geochemistry to identify ground-water flow paths. Relay ramps and associated faulting in northern Medina County appear to channel ground-water flow along four distinct flow paths that move water toward the southwest. The northwestern Medina flow path is bounded on the north by the Woodard Cave fault and on the south by the Parkers Creek fault. Water moves downdip toward the southwest until the flow encounters a cross fault along Seco Creek. This barrier to flow might force part or most of the flow to the south. Departure hydrographs for two wells and discharge departure for a streamflow-gaging station provide evidence for flow in the northwestern Medina flow path. The north-central Medina flow path (northern part) is bounded by the Parkers Creek fault on the north and the Medina Lake fault on the south. The adjacent north-central Medina flow path (southern part) is bounded on the north by the Medina Lake fault and on the south by the Diversion Lake fault. The north-central Medina flow path is separated into a northern and southern part because of water-level differences. Ground water in both parts of the northcentral Medina flow path moves downgradient (and down relay ramp) from eastern Medina County toward the southwest. The north-central Medina flow path is hypothesized to turn south in the vicinity of Seco Creek as it begins to be influenced by structural features. Departure hydrographs for four wells and Medina Lake and discharge departure for a streamflow-gaging station provide evidence for flow in the north-central Medina flow path. The south-central Medina flow path is bounded on the north by the Seco Creek and Diversion Lake faults and on the south by the Haby Crossing fault. Because of bounding faults oriented northeast-southwest and adjacent flow paths directed south by other geologic structures, the south-central Medina flow path follows the configuration of the adjacent flow paths—oriented initially southwest and then south. Immediately after turning south, the south-central Medina flow path turns sharply east. Departure hydrographs for four wells and discharge departure for a streamflow-gaging station provide evidence for flow in the south-central Medina flow path. Statistical correlations between water-level departures for 11 continuously monitored wells provide additional evidence for the hypothesized flow paths. Of the 55 combinations of departure dataset pairs, the stronger correlations (those greater than .6) are all among wells in the same flow path, with one exception. Simulations of compositional differences in water chemistry along a hypothesized flow path in the Edwards aquifer and between ground-water and surface-water systems near Medina Lake were developed using the geochemical model PHREEQC. Ground-water chemistry for samples from five wells in the Edwards aquifer in the northwestern Medina flow path were used to evaluate the evolution of ground-water chemistry in the northwestern Medina flow path. Seven simulations were done for samples from pairs of these wells collected during 2001–03; three of the seven yielded plausible models. Ground-water samples from 13 wells were used to evaluate the evolution of ground-water chemistry in the north-central Medina flow path (northern and southern parts). Five of the wells in the most upgradient part of the flow path were completed in the Trinity aquifer; the remaining eight were completed in the Edwards aquifer. Nineteen simulations were done for samples from well pairs collected during 1995–2003; eight of the 19 yielded plausible models. Ground-water samples from seven wells were used to evaluate the evolution of ground-water chemistry in the south-central Medina flow path. One well was the Trinity aquifer end-member well upgradient from all flow paths, and another was a Trinity aquifer well in the most upgradient part of the flow path; all other wells were completed in the Edwards aquifer. Nine simulations were done for samples from well pairs collected during 1996–2003; seven of the nine yielded plausible models. The plausible models demonstrate that the four hypothesized flow paths can be partially supported geochemically. 

Compatibility art of traditional Chinese medicine: from the perspective of herb pairs.

PubMed

Wang, Shengpeng; Hu, Yangyang; Tan, Wen; Wu, Xu; Chen, Ruie; Cao, Jiliang; Chen, Meiwan; Wang, Yitao

2012-09-28

Over the past decades, research of traditional Chinese medicine (TCM) mainly focused on developing potential candidates from Chinese medicinal herbs, while the wisdom of applying these traditional herbs has not been paid as much attention as it deserves. As is well-known, multi-herb therapy is one of the most important characteristics of TCM, but the modernization drive of this conventional wisdom has faced many obstacles due to its unimaginable complexity. Herb pairs, the most fundamental and the simplest form of multi-herb formulae, are a centralized representative of Chinese herbal compatibility. In light of their simplicity and the basic characteristics of complex formulae, herb pairs are of great importance in the studies of herb compatibility. A systematic search of herb pair related research was carried out using multiple online literature databases, books and monographs published in the past 20 years. A comprehensive introduction to the compatibility of TCM, the position of herb pairs in TCM and the progresses of several famous herb pairs were provided in this review. Furthermore, the clinical study and the future research trends of herb pairs were also discussed. Herb pairs have played, and may continue to play a key role in full investigation of general herb compatibility for their indispensable position in TCM. Much more research is needed for the standardization, safety evaluation, and mechanism exploration of herb pairs. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

The Crystal Structure of Non-Modified and Bipyridine-Modified PNA Duplexes

PubMed Central

Yeh, Joanne I.; Pohl, Ehmke; Truan, Daphne; He, Wei; Sheldrick, George M.; Du, Shoucheng; Achim, Catalina

2011-01-01

Peptide nucleic acid (PNA) is a synthetic analogue of DNA that commonly has an N-aminoethlyl-glycine backbone. The crystal structure of two PNA duplexes, one containing eight standard nucleobase pairs (GGCATCGG)2 (pdb: 3MBS), and the other containing the same nucleobase pairs and a central pair of bipyridine ligands (pdb: 3MBU), has been solved with a resolution of 1.2 Å and 1.05 Å, respectively. The non-modified PNA duplex adopts a P-type helical structure s i m i l a r t o that of previously characterized PNAs. The atomic-level resolution of the structures allowed us to observe for the first time specific modes of interaction between the terminal lysines of the PNA and the backbone and nucleobases situated in the vicinity of the lysines, which are considered an important factor in the induction of a preferred handedness in PNA duplexes. These results support the notion that while PNA typically adopts a P-type helical structure, its flexibility is relatively high. For example, the base pair rise in the bipyridine-containing PNA is the largest measured to date in a PNA homoduplex. The two bipyridines are bulged out of the duplex and are aligned parallel to the minor groove of the PNA. In the case of the bipyridine-containing PNA, two bipyridines from adjacent PNA duplexes form a π-stacked pair that relates the duplexes within the crystal. The bulging out of the bipyridines causes bending of the PNA duplex, which is in contrast to the structure previously reported for biphenyl-modified DNA duplexes in solution, where the biphenyls are π-stacking with adjacent nucleobase pairs and adopt an intrahelical geometry [Johar et al., Chem. Eur. J., 2008, 14, 2080]. This difference shows that relatively small perturbations can significantly impact the relative position of nucleobase analogues in nucleic acid duplexes. PMID:20859960

Rotational-translational fourier imaging system

NASA Technical Reports Server (NTRS)

Campbell, Jonathan W. (Inventor)

2004-01-01

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

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

PubMed

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

2011-03-14

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

PHOTOSPHERE EMISSION FROM A HYBRID RELATIVISTIC OUTFLOW WITH ARBITRARY DIMENSIONLESS ENTROPY AND MAGNETIZATION IN GRBs

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

Gao, He; Zhang, Bing, E-mail: gaohe@physics.unlv.edu, E-mail: zhang@physics.unlv.edu, E-mail: hug18@psu.edu

2015-03-10

In view of the recent Fermi observations of gamma-ray burst (GRB) prompt emission spectra, we develop a theory of photosphere emission of a hybrid relativistic outflow with a hot fireball component (defined by dimensionless entropy η) and a cold Poynting-flux component (defined by magnetization σ{sub 0} at the central engine). We consider the scenarios both without and with sub-photospheric magnetic dissipations. Based on a simplified toy model of jet dynamics, we develop two approaches: a 'bottom-up' approach to predict the temperature (for a non-dissipative photosphere) and luminosity of the photosphere emission and its relative brightness for a given pair ofmore » (η, σ{sub 0}); and a 'top-down' approach to diagnose central engine parameters (η and σ{sub 0}) based on the observed quasi-thermal photosphere emission properties. We show that a variety of observed GRB prompt emission spectra with different degrees of photosphere thermal emission can be reproduced by varying η and σ{sub 0} within the non-dissipative photosphere scenario. In order to reproduce the observed spectra, the outflows of most GRBs need to have a significant σ, both at the central engine and at the photosphere. The σ value at 10{sup 15} cm from the central engine (a possible non-thermal emission site) is usually also greater than unity, so that internal-collision-induced magnetic reconnection and turbulence (ICMART) may be the mechanism to power the non-thermal emission. We apply our top-down approach to GRB 110721A and find that the temporal evolution behavior of its blackbody component can be well interpreted with a time-varying (η, σ{sub 0}) at the central engine, instead of invoking a varying engine base size r {sub 0} as proposed by previous authors.« less

Molecular evidence for deep phylogenetic divergence in Mandrillus sphinx.

PubMed

Telfer, P T; Souquière, S; Clifford, S L; Abernethy, K A; Bruford, M W; Disotell, T R; Sterner, K N; Roques, P; Marx, P A; Wickings, E J

2003-07-01

Mandrills (Mandrillus sphinx) are forest primates indigenous to western central Africa. Phylogenetic analysis of 267 base pairs (bp) of the cytochrome b gene from 53 mandrills of known and 17 of unknown provenance revealed two phylogeographical groups, with haplotypes differentiated by 2.6% comprising seven synonymous transitions. The distribution of the haplotypes suggests that the Ogooué River, Gabon, which bisects their range, separates mandrill populations in Cameroon and northern Gabon from those in southern Gabon. The haplotype distribution is also concordant with that of two known mandrill simian immunodeficiency viruses, suggesting that these two mandrill phylogroups have followed different evolutionary trajectories since separation.

Efficient Implementation of the Pairing on Mobilephones Using BREW

NASA Astrophysics Data System (ADS)

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

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

Relative Modification of Prompt ψ ( 2 S ) and J / ψ Yields from p p to PbPb Collisions at s N N = 5.02 TeV

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

Sirunyan, A. M.; Tumasyan, A.; Adam, W.

The relative modification of the prompt ψ(2S) and J/ψ yields from pp to PbPb collisions, at the center-of-mass energy of 5.02 TeV per nucleon pair, is presented. The analysis is based on pp and PbPb data samples collected by the CMS experiment at the LHC in 2015, corresponding to integrated luminosities of 28.0 pb -1 and 464 μb -1, respectively. The double ratio of measured yields of prompt charmonia reconstructed through their decays into muon pairs, (N ψ(2S)/N J/ψ) PbPb/(N ψ(2S)/N J/ψ) pp, is determined as a function of PbPb collision centrality and charmonium transverse momentum p T, in two kinematicmore » intervals: |y|<1.6 covering 6.5< pT<30 GeV/c and 1.6<|y|<2.4 covering 3< pT<30 GeV/c. The centrality-integrated double ratios are 0.36 ± 0.08(stat) ±0.05 (syst) in the first interval and 0.24 ± 0.22(stat) ± 0.09 (syst) in the second. The double ratio is lower than unity in all the measured bins, suggesting that the ψ(2S) yield is more suppressed than the J/ψ yield in the explored phase space.« less

Relative Modification of Prompt ψ(2S) and J/ψ Yields from pp to PbPb Collisions at sqrt[s_{NN}]=5.02  TeV.

PubMed

Sirunyan, A M; Tumasyan, A; Adam, W; Asilar, E; Bergauer, T; Brandstetter, J; Brondolin, E; Dragicevic, M; Erö, J; Flechl, M; Friedl, M; Frühwirth, R; Ghete, V M; Hartl, C; Hörmann, N; Hrubec, J; Jeitler, M; König, A; Krätschmer, I; Liko, D; Matsushita, T; Mikulec, I; Rabady, D; Rad, N; Rahbaran, B; Rohringer, H; Schieck, J; Strauss, J; Waltenberger, W; Wulz, C-E; Chekhovsky, V; Dvornikov, O; Dydyshka, Y; Emeliantchik, I; Litomin, A; Makarenko, V; Mossolov, V; Stefanovitch, R; Suarez Gonzalez, J; Zykunov, V; Shumeiko, N; Alderweireldt, S; De Wolf, E A; Janssen, X; Lauwers, J; Van De Klundert, M; Van Haevermaet, H; Van Mechelen, P; Van Remortel, N; Van Spilbeeck, A; Abu Zeid, S; Blekman, F; D'Hondt, J; Daci, N; De Bruyn, I; Deroover, K; Lowette, S; Moortgat, S; Moreels, L; Olbrechts, A; Python, Q; Skovpen, K; Tavernier, S; Van Doninck, W; Van Mulders, P; Van Parijs, I; Brun, H; Clerbaux, B; De Lentdecker, G; Delannoy, H; Fasanella, G; Favart, L; Goldouzian, R; Grebenyuk, A; Karapostoli, G; Lenzi, T; Léonard, A; Luetic, J; Maerschalk, T; Marinov, A; Randle-Conde, A; Seva, T; Vander Velde, C; Vanlaer, P; Vannerom, D; Yonamine, R; Zenoni, F; Zhang, F; Cimmino, A; Cornelis, T; Dobur, D; Fagot, A; Garcia, G; Gul, M; Khvastunov, I; Poyraz, D; Salva, S; Schöfbeck, R; Tytgat, M; Van Driessche, W; Yazgan, E; Zaganidis, N; Bakhshiansohi, H; Beluffi, C; Bondu, O; Brochet, S; Bruno, G; Caudron, A; De Visscher, S; Delaere, C; Delcourt, M; Francois, B; Giammanco, A; Jafari, A; Jez, P; Komm, M; Krintiras, G; Lemaitre, V; Magitteri, A; Mertens, A; Musich, M; Nuttens, C; Piotrzkowski, K; Quertenmont, L; Selvaggi, M; Vidal Marono, M; Wertz, S; Beliy, N; Aldá Júnior, W L; Alves, F L; Alves, G A; Brito, L; Hensel, C; Moraes, A; Pol, M E; Rebello Teles, P; Belchior Batista Das Chagas, E; Carvalho, W; Chinellato, J; Custódio, A; Da Costa, E M; Da Silveira, G G; De Jesus Damiao, D; De Oliveira Martins, C; Fonseca De Souza, S; Huertas Guativa, L M; Malbouisson, H; Matos Figueiredo, D; Mora Herrera, C; Mundim, L; Nogima, H; Prado Da Silva, W L; Santoro, A; Sznajder, A; Tonelli Manganote, E J; Vilela Pereira, A; Ahuja, S; Bernardes, C A; Dogra, S; Tomei, T R Fernandez Perez; Gregores, E M; Mercadante, P G; Moon, C S; Novaes, S F; Padula, Sandra S; Romero Abad, D; Ruiz Vargas, J C; Aleksandrov, A; Hadjiiska, R; Iaydjiev, P; Rodozov, M; Stoykova, S; Sultanov, G; Vutova, M; Dimitrov, A; Glushkov, I; Litov, L; Pavlov, B; Petkov, P; Fang, W; Ahmad, M; Bian, J G; Chen, G M; Chen, H S; Chen, M; Chen, Y; Cheng, T; Jiang, C H; Leggat, D; Liu, Z; Romeo, F; Shaheen, S M; Spiezia, A; Tao, J; Wang, C; Wang, Z; Zhang, H; Zhao, J; Ban, Y; Chen, G; Li, Q; Liu, S; Mao, Y; Qian, S J; Wang, D; Xu, Z; Avila, C; Cabrera, A; Chaparro Sierra, L F; Florez, C; Gomez, J P; González Hernández, C F; Ruiz Alvarez, J D; Sanabria, J C; Godinovic, N; Lelas, D; Puljak, I; Ribeiro Cipriano, P M; Sculac, T; Antunovic, Z; Kovac, M; Brigljevic, V; Ferencek, D; Kadija, K; Mesic, B; Micanovic, S; Sudic, L; Susa, T; Attikis, A; Mavromanolakis, G; Mousa, J; Nicolaou, C; Ptochos, F; Razis, P A; Rykaczewski, H; Tsiakkouri, D; Finger, M; Finger, M; Carrera Jarrin, E; Ellithi Kamel, A; Mahmoud, M A; Radi, A; Kadastik, M; Perrini, L; Raidal, M; Tiko, A; Veelken, C; Eerola, P; Pekkanen, J; Voutilainen, M; Härkönen, J; Järvinen, T; Karimäki, V; Kinnunen, R; Lampén, T; Lassila-Perini, K; Lehti, S; Lindén, T; Luukka, P; Tuominiemi, J; Tuovinen, E; Wendland, L; Talvitie, J; Tuuva, T; Besancon, M; Couderc, F; Dejardin, M; Denegri, D; Fabbro, B; Faure, J L; Favaro, C; Ferri, F; Ganjour, S; Ghosh, S; Givernaud, A; Gras, P; Hamel de Monchenault, G; Jarry, P; Kucher, I; Locci, E; Machet, M; Malcles, J; Rander, J; Rosowsky, A; Titov, M; Zghiche, A; Abdulsalam, A; Antropov, I; Arleo, F; Baffioni, S; Beaudette, F; Busson, P; Cadamuro, L; Chapon, E; Charlot, C; Davignon, O; Granier de Cassagnac, R; Jo, M; Lisniak, S; Martin Blanco, J; Miné, P; Nguyen, M; Ochando, C; Ortona, G; Paganini, P; Pigard, P; Regnard, S; Salerno, R; Sirois, Y; Stahl Leiton, A G; Strebler, T; Yilmaz, Y; Zabi, A; Agram, J-L; Andrea, J; Aubin, A; Bloch, D; Brom, J-M; Buttignol, M; Chabert, E C; Chanon, N; Collard, C; Conte, E; Coubez, X; Fontaine, J-C; Gelé, D; Goerlach, U; Le Bihan, A-C; Van Hove, P; Gadrat, S; Beauceron, S; Bernet, C; Boudoul, G; Carrillo Montoya, C A; Chierici, R; Contardo, D; Courbon, B; Depasse, P; El Mamouni, H; Fan, J; Fay, J; Gascon, S; Gouzevitch, M; Grenier, G; Ille, B; Lagarde, F; Laktineh, I B; Lethuillier, M; Mirabito, L; Pequegnot, A L; Perries, S; Popov, A; Sabes, D; Sordini, V; Vander Donckt, M; Verdier, P; Viret, S; Toriashvili, T; Tsamalaidze, Z; Autermann, C; Beranek, S; Feld, L; Kiesel, M K; Klein, K; Lipinski, M; Preuten, M; Schael, S; Schomakers, C; Schulz, J; Verlage, T; Albert, A; Brodski, M; Dietz-Laursonn, E; Duchardt, D; Endres, M; Erdmann, M; Erdweg, S; Esch, T; Fischer, R; Güth, A; Hamer, M; Hebbeker, T; Heidemann, C; Hoepfner, K; Knutzen, S; Merschmeyer, M; Meyer, A; Millet, P; Mukherjee, S; Olschewski, M; Padeken, K; Pook, T; Radziej, M; Reithler, H; Rieger, M; Scheuch, F; Sonnenschein, L; Teyssier, D; Thüer, S; Cherepanov, V; Flügge, G; Kargoll, B; Kress, T; Künsken, A; Lingemann, J; Müller, T; Nehrkorn, A; Nowack, A; Pistone, C; Pooth, O; Stahl, A; Aldaya Martin, M; Arndt, T; Asawatangtrakuldee, C; Beernaert, K; Behnke, O; Behrens, U; Bin Anuar, A A; Borras, K; Campbell, A; Connor, P; Contreras-Campana, C; Costanza, F; Diez Pardos, C; Dolinska, G; Eckerlin, G; Eckstein, D; Eichhorn, T; Eren, E; Gallo, E; Garay Garcia, J; Geiser, A; Gizhko, A; Grados Luyando, J M; Grohsjean, A; Gunnellini, P; Harb, A; Hauk, J; Hempel, M; Jung, H; Kalogeropoulos, A; Karacheban, O; Kasemann, M; Keaveney, J; Kleinwort, C; Korol, I; Krücker, D; Lange, W; Lelek, A; Leonard, J; Lipka, K; Lobanov, A; Lohmann, W; Mankel, R; Melzer-Pellmann, I-A; Meyer, A B; Mittag, G; Mnich, J; Mussgiller, A; Ntomari, E; Pitzl, D; Placakyte, R; Raspereza, A; Roland, B; Sahin, M Ö; Saxena, P; Schoerner-Sadenius, T; Seitz, C; Spannagel, S; Stefaniuk, N; Van Onsem, G P; Walsh, R; Wissing, C; Blobel, V; Centis Vignali, M; Draeger, A R; Dreyer, T; Garutti, E; Gonzalez, D; Haller, J; Hoffmann, M; Junkes, A; Klanner, R; Kogler, R; Kovalchuk, N; Lapsien, T; Lenz, T; Marchesini, I; Marconi, D; Meyer, M; Niedziela, M; Nowatschin, D; Pantaleo, F; Peiffer, T; Perieanu, A; Poehlsen, J; Sander, C; Scharf, C; Schleper, P; Schmidt, A; Schumann, S; Schwandt, J; Stadie, H; Steinbrück, G; Stober, F M; Stöver, M; Tholen, H; Troendle, D; Usai, E; Vanelderen, L; Vanhoefer, A; Vormwald, B; Akbiyik, M; Barth, C; Baur, S; Baus, C; Berger, J; Butz, E; Caspart, R; Chwalek, T; Colombo, F; De Boer, W; Dierlamm, A; Fink, S; Freund, B; Friese, R; Giffels, M; Gilbert, A; Goldenzweig, P; Haitz, D; Hartmann, F; Heindl, S M; Husemann, U; Katkov, I; Kudella, S; Mildner, H; Mozer, M U; Müller, Th; Plagge, M; Quast, G; Rabbertz, K; Röcker, S; Roscher, F; Schröder, M; Shvetsov, I; Sieber, G; Simonis, H J; Ulrich, R; Wayand, S; Weber, M; Weiler, T; Williamson, S; 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Wright, D; Anelli, C; Baden, A; Baron, O; Belloni, A; Calvert, B; Eno, S C; Ferraioli, C; Gomez, J A; Hadley, N J; Jabeen, S; Kellogg, R G; Kolberg, T; Kunkle, J; Lu, Y; Mignerey, A C; Ricci-Tam, F; Shin, Y H; Skuja, A; Tonjes, M B; Tonwar, S C; Abercrombie, D; Allen, B; Apyan, A; Azzolini, V; Barbieri, R; Baty, A; Bi, R; Bierwagen, K; Brandt, S; Busza, W; Cali, I A; D'Alfonso, M; Demiragli, Z; Di Matteo, L; Gomez Ceballos, G; Goncharov, M; Hsu, D; Iiyama, Y; Innocenti, G M; Klute, M; Kovalskyi, D; Krajczar, K; Lai, Y S; Lee, Y-J; Levin, A; Luckey, P D; Maier, B; Marini, A C; Mcginn, C; Mironov, C; Narayanan, S; Niu, X; Paus, C; Roland, C; Roland, G; Salfeld-Nebgen, J; Stephans, G S F; Tatar, K; Varma, M; Velicanu, D; Veverka, J; Wang, J; Wang, T W; Wyslouch, B; Yang, M; Zhukova, V; Benvenuti, A C; Chatterjee, R M; Evans, A; Finkel, A; Gude, A; Hansen, P; Kalafut, S; Kao, S C; Kubota, Y; Lesko, Z; Mans, J; Nourbakhsh, S; Ruckstuhl, N; Rusack, R; Tambe, N; Turkewitz, J; Acosta, J G; Oliveros, S; Avdeeva, E; Bartek, R; Bloom, K; Claes, D R; Dominguez, A; Fangmeier, C; Gonzalez Suarez, R; Kamalieddin, R; Kravchenko, I; Malta Rodrigues, A; Meier, F; Monroy, J; Siado, J E; Snow, G R; Stieger, B; Alyari, M; Dolen, J; George, J; Godshalk, A; Harrington, C; Iashvili, I; Kaisen, J; Kharchilava, A; Kumar, A; Parker, A; Rappoccio, S; Roozbahani, B; Alverson, G; Barberis, E; Hortiangtham, A; Massironi, A; Morse, D M; Nash, D; Orimoto, T; Teixeira De Lima, R; Trocino, D; Wang, R-J; Wood, D; Bhattacharya, S; Charaf, O; Hahn, K A; Kubik, A; Kumar, A; Mucia, N; Odell, N; Pollack, B; Schmitt, M H; Sung, K; Trovato, M; Velasco, M; Dev, N; Hildreth, M; Hurtado Anampa, K; Jessop, C; Karmgard, D J; Kellams, N; Lannon, K; Marinelli, N; Meng, F; Mueller, C; Musienko, Y; Planer, M; Reinsvold, A; Ruchti, R; Smith, G; Taroni, S; Wayne, M; Wolf, M; Woodard, A; Alimena, J; Antonelli, L; Bylsma, B; Durkin, L S; Flowers, S; Francis, B; Hart, A; Hill, C; Hughes, R; Ji, W; Liu, B; Luo, W; Puigh, D; Winer, B L; Wulsin, H W; Cooperstein, S; Driga, O; Elmer, P; Hardenbrook, J; Hebda, P; Lange, D; Luo, J; Marlow, D; Medvedeva, T; Mei, K; Mooney, M; Olsen, J; Palmer, C; Piroué, P; Stickland, D; Svyatkovskiy, A; Tully, C; Zuranski, A; Malik, S; Barker, A; Barnes, V E; Folgueras, S; Gutay, L; Jha, M K; Jones, M; Jung, A W; Khatiwada, A; Miller, D H; Neumeister, N; Schulte, J F; Shi, X; Sun, J; Wang, F; Xie, W; Parashar, N; Stupak, J; Adair, A; Akgun, B; Chen, Z; Ecklund, K M; Geurts, F J M; Guilbaud, M; Li, W; Michlin, B; Northup, M; Padley, B P; Redjimi, R; Roberts, J; Rorie, J; Tu, Z; Zabel, J; Betchart, B; Bodek, A; de Barbaro, P; Demina, R; Duh, Y T; Ferbel, T; Galanti, M; Garcia-Bellido, A; Han, J; Hindrichs, O; Khukhunaishvili, A; Lo, K H; Tan, P; Verzetti, M; Agapitos, A; Chou, J P; Contreras-Campana, E; Gershtein, Y; Gómez Espinosa, T A; Halkiadakis, E; Heindl, M; Hidas, D; Hughes, E; Kaplan, S; Kunnawalkam Elayavalli, R; Kyriacou, S; Lath, A; Nash, K; Saka, H; Salur, S; Schnetzer, S; Sheffield, D; Somalwar, S; Stone, R; Thomas, S; Thomassen, P; Walker, M; Delannoy, A G; Foerster, M; Heideman, J; Riley, G; Rose, K; Spanier, S; Thapa, K; Bouhali, O; Celik, A; Dalchenko, M; De Mattia, M; Delgado, A; Dildick, S; Eusebi, R; Gilmore, J; Huang, T; Juska, E; Kamon, T; Mueller, R; Pakhotin, Y; Patel, R; Perloff, A; Perniè, L; Rathjens, D; Rose, A; Safonov, A; Tatarinov, A; Ulmer, K A; Akchurin, N; Cowden, C; Damgov, J; De Guio, F; Dragoiu, C; Dudero, P R; Faulkner, J; Gurpinar, E; Kunori, S; Lamichhane, K; Lee, S W; Libeiro, T; Peltola, T; Undleeb, S; Volobouev, I; Wang, Z; Greene, S; Gurrola, A; Janjam, R; Johns, W; Maguire, C; Melo, A; Ni, H; Sheldon, P; Tuo, S; Velkovska, J; Xu, Q; Arenton, M W; Barria, P; Cox, B; Goodell, J; Hirosky, R; Ledovskoy, A; Li, H; Neu, C; Sinthuprasith, T; Sun, X; Wang, Y; Wolfe, E; Xia, F; Clarke, C; Harr, R; Karchin, P E; Sturdy, J; Belknap, D A; Buchanan, J; Caillol, C; Dasu, S; Dodd, L; Duric, S; Gomber, B; Grothe, M; Herndon, M; Hervé, A; Klabbers, P; Lanaro, A; Levine, A; Long, K; Loveless, R; Ojalvo, I; Perry, T; Pierro, G A; Polese, G; Ruggles, T; Savin, A; Smith, N; Smith, W H; Taylor, D; Woods, N

2017-04-21

The relative modification of the prompt ψ(2S) and J/ψ yields from pp to PbPb collisions, at the center-of-mass energy of 5.02 TeV per nucleon pair, is presented. The analysis is based on pp and PbPb data samples collected by the CMS experiment at the LHC in 2015, corresponding to integrated luminosities of 28.0  pb^{-1} and 464  μb^{-1}, respectively. The double ratio of measured yields of prompt charmonia reconstructed through their decays into muon pairs, (N_{ψ(2S)}/N_{J/ψ})_{PbPb}/(N_{ψ(2S)}/N_{J/ψ})_{pp}, is determined as a function of PbPb collision centrality and charmonium transverse momentum p_{T}, in two kinematic intervals: |y|<1.6 covering 6.5

Relative Modification of Prompt ψ ( 2 S ) and J / ψ Yields from p p to PbPb Collisions at s N N = 5.02 TeV

DOE PAGES

Sirunyan, A. M.; Tumasyan, A.; Adam, W.; ...

2017-04-20

The relative modification of the prompt ψ(2S) and J/ψ yields from pp to PbPb collisions, at the center-of-mass energy of 5.02 TeV per nucleon pair, is presented. The analysis is based on pp and PbPb data samples collected by the CMS experiment at the LHC in 2015, corresponding to integrated luminosities of 28.0 pb -1 and 464 μb -1, respectively. The double ratio of measured yields of prompt charmonia reconstructed through their decays into muon pairs, (N ψ(2S)/N J/ψ) PbPb/(N ψ(2S)/N J/ψ) pp, is determined as a function of PbPb collision centrality and charmonium transverse momentum p T, in two kinematicmore » intervals: |y|<1.6 covering 6.5< pT<30 GeV/c and 1.6<|y|<2.4 covering 3< pT<30 GeV/c. The centrality-integrated double ratios are 0.36 ± 0.08(stat) ±0.05 (syst) in the first interval and 0.24 ± 0.22(stat) ± 0.09 (syst) in the second. The double ratio is lower than unity in all the measured bins, suggesting that the ψ(2S) yield is more suppressed than the J/ψ yield in the explored phase space.« less

e+e‑ Pair Production at Very Low Transverse Mometum in Au+Au Collisions at s NN = 200 GeV and U+U Collisions at sNN = 193 GeV at STAR

NASA Astrophysics Data System (ADS)

Yang, Shuai

We present the first measurements of e+e‑ pair production at very low transverse momentum (pT < 0.15 GeV/c) in Au + Au collisions at sNN = 200 GeV and U + U collisions at sNN = 193 GeV using the STAR detector at the Relativistic Heavy Ion Collider. A significant excess, with respect to known hadronic contributions, is observed in 60-80% central heavy-ion collisions over the whole Mee range. Remarkably, the excess almost entirely happens below pT ≈ 0.15 GeV/c, and can not be explained by a theoretical model calculation incorporating in-medium broadened ρ spectral function. Moreover, the observed excess yield has no significant centrality dependence. In addition, the steepness of pT2 distribution exhibits mild invariant mass and collision species dependence.

Clamp-mount device

NASA Technical Reports Server (NTRS)

Clark, K. H. (Inventor)

1983-01-01

A clamp-mount device is disclosed for mounting equipment to an associated I-beam and the like structural member of the type having oppositely extending flanges wherein the device comprises a base and a pair of oppositely facing clamping members carried diagonally on the base clamping flanges therebetween and having flange receiving openings facing one another. Lock means are carried diagonally by the base opposite the clamping members locking the flanges in the clamping members. A resilient hub is carried centrally of the base engaging and biasing a back side of the flanges maintaining tightly clamped and facilitating use on vertical as well as horizontal members. The base turns about the hub to receive the flanges within the clamping members. Equipment may be secured to the base by any suitable means such as bolts in openings. Slidable gate latches secure the hinged locks in an upright locking position. The resilient hub includes a recess opening formed in the base and a rubber-like pad carried in this opening being depressably and rotatably carried therein.

Genetic covariance between central corneal thickness and anterior chamber volume: a Hungarian twin study.

PubMed

Toth, Georgina Zsofia; Racz, Adel; Tarnoki, Adam Domonkos; Tarnoki, David Laszlo; Szekelyhidi, Zita; Littvay, Levente; Suveges, Ildiko; Nemeth, Janos; Nagy, Zoltan Zsolt

2014-10-01

Few, and inconsistent, studies have showed high heritability of some parameters of the anterior segment of the eye; however, no heritability of anterior chamber volume (ACV) has been reported, and no study has been performed to investigate the correlation between the ACV and central corneal thickness (CCT). Anterior segment measurements (Pentacam, Oculus) were obtained from 220 eyes of 110 adult Hungarian twins (41 monozygotic and 14 same-sex dizygotic pairs; 80% women; age 48.6 ± 15.5 years) obtained from the Hungarian Twin Registry. Age- and sex-adjusted heritability of ACV was 85% (bootstrapped 95% confidence interval; CI: 69% to 93%), and 88% for CCT (CI: 79% to 95%). Common environmental effects had no influence, and unshared environmental factors were responsible for 12% and 15% of the variance, respectively. The correlation between ACV and CCT was negative and significant (r ph = -0.35, p < .05), and genetic factors accounted for the covariance significantly (0.934; CI: 0.418, 1.061) based on the bivariate Cholesky decomposition model. These findings support the high heritability of ACV and central corneal thickness, and a strong genetic covariance between them, which underscores the importance of identification of the specific genetic factors and the family risk-based screening of disorders related to these variables, such as open-angle and also angle closure glaucoma and corneal endothelial alterations.

An ensemble of SVM classifiers based on gene pairs.

PubMed

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

2013-07-01

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

Optogenetic excitation of central amygdala amplifies and narrows incentive motivation to pursue one reward above another.

PubMed

Robinson, Mike J F; Warlow, Shelley M; Berridge, Kent C

2014-12-10

Choosing one reward above another is important for achieving adaptive life goals. Yet hijacked into excessive intensity in disorders such as addiction, single-minded pursuit becomes maladaptive. Here, we report that optogenetic channelrhodopsin stimulation of neurons in central nucleus of amygdala (CeA), paired with earning a particular sucrose reward in rats, amplified and narrowed incentive motivation to that single reward target. Therefore, CeA rats chose and intensely pursued only the laser-paired sucrose reward while ignoring an equally good sucrose alternative. In contrast, reward-paired stimulation of basolateral amygdala did not hijack choice. In a separate measure of incentive motivation, CeA stimulation also increased the progressive ratio breakpoint or level of effort exerted to obtain sucrose reward. However, CeA stimulation by itself failed to support behavioral self-stimulation in the absence of any paired external food reward, suggesting that CeA photo-excitation specifically transformed the value of its external reward (rather than adding an internal reinforcement state). Nor did CeA stimulation by itself induce any aversive state that motivated escape. Finally, CeA stimulation also failed to enhance 'liking' reactions elicited by sucrose taste and did not simply increase the general motivation to eat. This pattern suggests that CeA photo-excitation specifically enhances and narrows incentive motivation to pursue an associated external reward at the expense of another comparable reward. Copyright © 2014 the authors 0270-6474/14/3416567-14$15.00/0.

Post-Traumatic Stress Avoidance is Attenuated by Corticosterone and Associated with Brain Levels of Steroid Receptor Co-Activator-1 in Rats

PubMed Central

Whitaker, Annie M.; Farooq, Muhammad A.; Edwards, Scott; Gilpin, Nicholas W.

2016-01-01

Individuals with post-traumatic stress disorder (PTSD) avoid trauma-related stimuli and exhibit blunted hypothalamic-pituitary-adrenal (HPA) axis activation at the time of stress. Our laboratory has established a rodent model of stress that mimics the avoidance symptom cluster of PTSD. Rats are classified as ‘Avoiders’ or ‘Non-Avoiders’ post-stress based on avoidance of a predator-odor paired context. Previously, we demonstrated that Avoiders exhibit an attenuated HPA stress response to predator odor. We hypothesized that corticosterone administration prior to stress would reduce magnitude and incidence of avoidance of a stress-paired context. Furthermore, we predicted that Avoiders would exhibit altered expression of GR signaling machinery elements, such as steroid receptor co-activator (SRC)-1. Male Wistar rats (n = 16) were pre-treated with corticosterone (25 mg/kg) or saline and exposed to predator odor stress paired with a context, and tested for avoidance 24 h later, A second group of corticosterone-naïve rats (n = 24) were stressed (or not stressed), indexed for avoidance 24 h later, and killed 48 h post-odor exposure for analysis of phosphorylated GR, FKBP51, and SRC-1 levels in the paraventricular nucleus (PVN), central amygdala (CeA) and ventral hippocampus (VH), all brain sites that express high quantities of GRs and regulate HPA function. Rats pre-treated with corticosterone exhibited lower magnitude and incidence of avoidance. Predator odor exposure also reduced SRC-1 expression in the PVN and CeA of Avoiders, and increased SRC-1 expression in the VH of Avoiders. SRC-1 expression in PVN, CeA, and VH was predicted by prior avoidance behavior. These results suggest that blunted HPA stress response may contribute to stress-induced neuroadaptations in central SRC-1 levels and behavioral dysfunction in Avoider rats. PMID:26482332

Envisaging quantum transport phenomenon in a muddled base pair of DNA

NASA Astrophysics Data System (ADS)

Vohra, Rajan; Sawhney, Ravinder Singh

2018-05-01

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

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

PubMed Central

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

2014-01-01

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

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

PubMed

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

2015-10-12

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

Molecular switching behavior in isosteric DNA base pairs.

PubMed

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

2013-04-15

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

Use of two sulfonthalein dyes in the extraction-free spectrophotometric assay of tramadol in dosage forms and in spiked human urine based on ion-pair reaction.

PubMed

Vinay, Kanakapura B; Revannasiddappa, Hosakere D; Rajendraprasad, Nagaraju; Ramesh, Pavagada J; Xavier, Cijo M; Basavaiah, Kanakapura

2012-02-01

Tramadol is a centrally acting analgesic used in the prevention and treatment of moderate to severe pain. Two sensitive, selective, and rapid spectrophotometric methods are described for the determination of tramadol in its dosage forms and in spiked human urine. The methods are based on formation of yellow ion-pairs between tramadol and two sulfonthalein dyes; bromocresol purple (BCP) and bromocresol green (BCG) in dichloromethane medium followed by absorbance measurement at 400 and 410 nm, respectively. Under the optimum conditions, tramadol could be assayed in the concentration ranges, 1-15 and 1-16 µg ml(-1) with correlation coefficient greater than 0.999 in both cases. The molar absorptivity values are calculated to be 1.84 × 10(4) and 1.97 × 10(4) l mol(-1) cm(-1) for BCP and BCG methods, respectively; and the corresponding Sandell sensitivity values are 0.0143 and 0.0134 µg cm(-2). The limits of detection (LOD) and quantification (LOQ) have also been reported. The stoichiometry of the reaction was found to be 1:1 in both cases and the conditional stability constant (K(f)) values of the ion pairs have been calculated. The within-day and between-day RSD were 0.9-1.96% and 1.56-3.21%, respectively. The methods were successfully applied to the determination of tramadol in tablets and injections and also in spiked human urine with good recoveries. The procedures are simple, accurate, and suitable for quality control application. Copyright © 2011 John Wiley & Sons, Ltd.

Validation of a semi-automatic protocol for the assessment of the tear meniscus central area based on open-source software

NASA Astrophysics Data System (ADS)

Pena-Verdeal, Hugo; Garcia-Resua, Carlos; Yebra-Pimentel, Eva; Giraldez, Maria J.

2017-08-01

Purpose: Different lower tear meniscus parameters can be clinical assessed on dry eye diagnosis. The aim of this study was to propose and analyse the variability of a semi-automatic method for measuring lower tear meniscus central area (TMCA) by using open source software. Material and methods: On a group of 105 subjects, one video of the lower tear meniscus after fluorescein instillation was generated by a digital camera attached to a slit-lamp. A short light beam (3x5 mm) with moderate illumination in the central portion of the meniscus (6 o'clock) was used. Images were extracted from each video by a masked observer. By using an open source software based on Java (NIH ImageJ), a further observer measured in a masked and randomized order the TMCA in the short light beam illuminated area by two methods: (1) manual method, where TMCA images was "manually" measured; (2) semi-automatic method, where TMCA images were transformed in an 8-bit-binary image, then holes inside this shape were filled and on the isolated shape, the area size was obtained. Finally, both measurements, manual and semi-automatic, were compared. Results: Paired t-test showed no statistical difference between both techniques results (p = 0.102). Pearson correlation between techniques show a significant positive near to perfect correlation (r = 0.99; p < 0.001). Conclusions: This study showed a useful tool to objectively measure the frontal central area of the meniscus in photography by free open source software.

Evaluating the accuracy of sampling to estimate central line-days: simplification of the National Healthcare Safety Network surveillance methods.

PubMed

Thompson, Nicola D; Edwards, Jonathan R; Bamberg, Wendy; Beldavs, Zintars G; Dumyati, Ghinwa; Godine, Deborah; Maloney, Meghan; Kainer, Marion; Ray, Susan; Thompson, Deborah; Wilson, Lucy; Magill, Shelley S

2013-03-01

To evaluate the accuracy of weekly sampling of central line-associated bloodstream infection (CLABSI) denominator data to estimate central line-days (CLDs). Obtained CLABSI denominator logs showing daily counts of patient-days and CLD for 6-12 consecutive months from participants and CLABSI numerators and facility and location characteristics from the National Healthcare Safety Network (NHSN). Convenience sample of 119 inpatient locations in 63 acute care facilities within 9 states participating in the Emerging Infections Program. Actual CLD and estimated CLD obtained from sampling denominator data on all single-day and 2-day (day-pair) samples were compared by assessing the distributions of the CLD percentage error. Facility and location characteristics associated with increased precision of estimated CLD were assessed. The impact of using estimated CLD to calculate CLABSI rates was evaluated by measuring the change in CLABSI decile ranking. The distribution of CLD percentage error varied by the day and number of days sampled. On average, day-pair samples provided more accurate estimates than did single-day samples. For several day-pair samples, approximately 90% of locations had CLD percentage error of less than or equal to ±5%. A lower number of CLD per month was most significantly associated with poor precision in estimated CLD. Most locations experienced no change in CLABSI decile ranking, and no location's CLABSI ranking changed by more than 2 deciles. Sampling to obtain estimated CLD is a valid alternative to daily data collection for a large proportion of locations. Development of a sampling guideline for NHSN users is underway.

Recruitment of rat diaphragm motor units across motor behaviors with different levels of diaphragm activation.

PubMed

Seven, Yasin B; Mantilla, Carlos B; Sieck, Gary C

2014-12-01

Phrenic motor neurons are recruited across a range of motor behaviors to generate varying levels of diaphragm muscle (DIAm) force. We hypothesized that DIAm motor units are recruited in a fixed order across a range of motor behaviors of varying force levels, consistent with the Henneman Size Principle. Single motor unit action potentials and compound DIAm EMG activities were recorded in anesthetized, neurally intact rats across different motor behaviors, i.e., eupnea, hypoxia-hypercapnia (10% O2 and 5% CO2), deep breaths, sustained airway occlusion, and sneezing. Central drive [estimated by root-mean-squared (RMS) EMG value 75 ms after the onset of EMG activity (RMS75)], recruitment delay, and onset discharge frequencies were similar during eupnea and hypoxia-hypercapnia. Compared with eupnea, central drive increased (∼25%) during deep breaths, and motor units were recruited ∼12 ms earlier (P < 0.01). During airway occlusion, central drive was ∼3 times greater, motor units were recruited ∼30 ms earlier (P < 0.01), and motor unit onset discharge frequencies were significantly higher (P < 0.01). Recruitment order of motor unit pairs observed during eupnea was maintained for 98%, 87%, and 84% of the same pairs recorded during hypoxia-hypercapnia, deep breaths, and airway occlusion, respectively. Reversals in motor unit recruitment order were observed primarily if motor unit pairs were recruited <20 ms apart. These results are consistent with DIAm motor unit recruitment order being determined primarily by the intrinsic size-dependent electrophysiological properties of phrenic motor neurons. Copyright © 2014 the American Physiological Society.

Recruitment of rat diaphragm motor units across motor behaviors with different levels of diaphragm activation

PubMed Central

Seven, Yasin B.; Mantilla, Carlos B.

2014-01-01

Phrenic motor neurons are recruited across a range of motor behaviors to generate varying levels of diaphragm muscle (DIAm) force. We hypothesized that DIAm motor units are recruited in a fixed order across a range of motor behaviors of varying force levels, consistent with the Henneman Size Principle. Single motor unit action potentials and compound DIAm EMG activities were recorded in anesthetized, neurally intact rats across different motor behaviors, i.e., eupnea, hypoxia-hypercapnia (10% O2 and 5% CO2), deep breaths, sustained airway occlusion, and sneezing. Central drive [estimated by root-mean-squared (RMS) EMG value 75 ms after the onset of EMG activity (RMS75)], recruitment delay, and onset discharge frequencies were similar during eupnea and hypoxia-hypercapnia. Compared with eupnea, central drive increased (∼25%) during deep breaths, and motor units were recruited ∼12 ms earlier (P < 0.01). During airway occlusion, central drive was ∼3 times greater, motor units were recruited ∼30 ms earlier (P < 0.01), and motor unit onset discharge frequencies were significantly higher (P < 0.01). Recruitment order of motor unit pairs observed during eupnea was maintained for 98%, 87%, and 84% of the same pairs recorded during hypoxia-hypercapnia, deep breaths, and airway occlusion, respectively. Reversals in motor unit recruitment order were observed primarily if motor unit pairs were recruited <20 ms apart. These results are consistent with DIAm motor unit recruitment order being determined primarily by the intrinsic size-dependent electrophysiological properties of phrenic motor neurons. PMID:25257864

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

PubMed

Liang, Feng; Lindsay, Stuart; Zhang, Peiming

2012-11-21

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

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

PubMed Central

Liang, Feng; Lindsay, Stuart; Zhang, Peiming

2013-01-01

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

Toward rules relating zinc finger protein sequences and DNA binding site preferences.

PubMed

Desjarlais, J R; Berg, J M

1992-08-15

Zinc finger proteins of the Cys2-His2 type consist of tandem arrays of domains, where each domain appears to contact three adjacent base pairs of DNA through three key residues. We have designed and prepared a series of variants of the central zinc finger within the DNA binding domain of Sp1 by using information from an analysis of a large data base of zinc finger protein sequences. Through systematic variations at two of the three contact positions (underlined), relatively specific recognition of sequences of the form 5'-GGGGN(G or T)GGG-3' has been achieved. These results provide the basis for rules that may develop into a code that will allow the design of zinc finger proteins with preselected DNA site specificity.

Drum tie-down apparatus

DOEpatents

Morse, H.E.

A drum tie-down apparatus for securing drum-like containers in an upright position to a floor or platform of a transportation vehicle having spaced apart cargo tie-down points. The apparatus comprises a pair of cylindrical, hollow tube segments horizontally oriented and engageable with a drum lid adjacent opposite rim edges, flexible strap segments for connecting upper and lower central portions of the tube segments together across the drum lid and a pair of elongated flexible tie-down segments, one extending horizontally through each of the tube segments, the ends thereof being attached to said spaced apart tie-down points such that end portions of the pair of tie-down segments extend downwardly and radially outwardly from the tube segments to the tie-down points.

Drum tie-down apparatus

DOEpatents

Morse, Harvey E.

1984-01-01

A drum tie-down apparatus for securing drum-like containers in an upright position to a floor or platform of a transportation vehicle having spaced apart cargo tie-down points. The apparatus comprises a pair of cylindrical, hollow tube segments horizontally oriented and engageable with a drum lid adjacent opposite rim edges, flexible strap segments for connecting upper and lower central portions of the tube segments together across the drum lid and a pair of elongated flexible tie-down segments, one extending horizontally through each of the tube segments, the ends thereof being attached to said spaced apart tie-down points such that end portions of the pair of tie-down segments extend downwardly and radially outwardly from the tube segments to the tie-down points.

A genomically modified Escherichia coli strain carrying an orthogonal E. coli histidyl-tRNA synthetase•tRNAHis pair.

PubMed

Englert, Markus; Vargas-Rodriguez, Oscar; Reynolds, Noah M; Wang, Yane-Shih; Söll, Dieter; Umehara, Takuya

2017-11-01

Development of new aminoacyl-tRNA synthetase (aaRS)•tRNA pairs is central for incorporation of novel non-canonical amino acids (ncAAs) into proteins via genetic code expansion (GCE). The Escherichia coli and Caulobacter crescentus histidyl-tRNA synthetases (HisRS) evolved divergent mechanisms of tRNA His recognition that prevent their cross-reactivity. Although the E. coli HisRS•tRNA His pair is a good candidate for GCE, its use in C. crescentus is limited by the lack of established genetic selection methods and by the low transformation efficiency of C. crescentus. E. coli was genetically engineered to use a C. crescentus HisRS•tRNA His pair. Super-folder green fluorescent protein (sfGFP) and chloramphenicol acetyltransferase (CAT) were used as reporters for read-through assays. A library of 313 ncAAs coupled with the sfGFP reporter system was employed to investigate the specificity of E. coli HisRS in vivo. A genomically modified E. coli strain (named MEOV1) was created. MEVO1 requires an active C. crescentus HisRS•tRNA His pair for growth, and displays a similar doubling time as the parental E. coli strain. sfGFP- and CAT-based assays showed that the E. coli HisRS•tRNA His pair is orthogonal in MEOV1 cells. A mutation in the anticodon loop of E. coli tRNA His CUA elevated its suppression efficiency by 2-fold. The C. crescentus HisRS•tRNA His pair functionally complements an E. coli ΔhisS strain. The E. coli HisRS•tRNA His is orthogonal in MEOV1 cells. E. coli tRNA His CUA is an efficient amber suppressor in MEOV1. We developed a platform that allows protein engineering of E. coli HisRS that should facilitate GCE in E. coli. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue. Copyright © 2017 Elsevier B.V. All rights reserved.

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

PubMed

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

2013-06-17

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

Central venous catheter - flushing

MedlinePlus

... on a pair of sterile gloves. Remove the cap on the saline syringe and set the cap down on the paper towel. DO NOT let ... It is a good idea to change the caps at the end of your catheter (called the " ...

Peripherally inserted central catheter - flushing

MedlinePlus

... on a pair of sterile gloves. Remove the cap on the saline syringe and set the cap down on the paper towel. DO NOT let ... It is a good idea to change the caps at the end of your catheter (called the " ...

Responses of a Federally Endangered Songbird to Understory Thinning in Oak-Juniper Woodlands

NASA Astrophysics Data System (ADS)

Long, Ashley M.; Marshall, Mike E.; Morrison, Michael L.; Hays, K. Brian; Farrell, Shannon L.

2017-04-01

Wildlife conservation and management on military lands must be accomplished in the context of military readiness, which often includes ground-based training that is perceived to conflict with wildlife needs and environmental regulations. From 2008‒2012, we examined territory density, pairing success, and fledging success of the federally endangered golden-cheeked warbler ( Setophaga chrysoparia; hereafter warbler) in relation to removal of small-diameter trees from the understory of mature oak-juniper ( Quercus-Juniperus) woodland at the 87,890 ha Fort Hood Military Reservation in central Texas. Understory thinning created troop maneuver lanes, but left canopy vegetation intact. Warbler density, pairing success, and fledging success were similar across thinned and control sites. We found that warbler pairing and fledging success were best predicted by Ecological site (hereafter Ecosite), an indicator of hardwood tree species composition. Warbler pairing and fledging success were about 1.5 and 1.6 times higher, respectively, for territories dominated by the Low Stony Hill Ecosite than territories dominated by the Redlands Ecosite. Our results indicate that understory thinning for military training purposes did not have a negative effect on warblers at Fort Hood in the manner tested, and suggest that removal of smaller trees from the understory in a way that replicates historic conditions may elicit neutral responses from this forest-dependent songbird. Quantifying wildlife responses to military activities provides the Department of Defense and US Fish and Wildlife Service with data to guide conservation of threatened and endangered species on Department of Defense facilities while maintaining the military mission, and supports wildlife management efforts on other public and private lands.

Standing chromosomal variation in Lake Whitefish species pairs: the role of historical contingency and relevance for speciation.

PubMed

Dion-Côté, Anne-Marie; Symonová, Radka; Lamaze, Fabien C; Pelikánová, Šárka; Ráb, Petr; Bernatchez, Louis

2017-01-01

The role of chromosome changes in speciation remains a debated topic, although demographic conditions associated with divergence should promote their appearance. We tested a potential relationship between chromosome changes and speciation by studying two Lake Whitefish (Coregonus clupeaformis) lineages that recently colonized postglacial lakes following allopatry. A dwarf limnetic species evolved repeatedly from the normal benthic species, becoming reproductively isolated. Lake Whitefish hybrids experience mitotic and meiotic instability, which may result from structurally divergent chromosomes. Motivated by this observation, we test the hypothesis that chromosome organization differs between Lake Whitefish species pairs using cytogenetics. While chromosome and fundamental numbers are conserved between the species (2n = 80, NF = 98), we observe extensive polymorphism of subtle karyotype traits. We describe intrachromosomal differences associated with heterochromatin and repetitive DNA, and test for parallelism among three sympatric species pairs. Multivariate analyses support the hypothesis that differentiation at the level of subchromosomal markers mostly appeared during allopatry. Yet we find no evidence for parallelism between species pairs among lakes, consistent with colonization effect or postcolonization differentiation. The reported intrachromosomal polymorphisms do not appear to play a central role in driving adaptive divergence between normal and dwarf Lake Whitefish. We discuss how chromosomal differentiation in the Lake Whitefish system may contribute to the destabilization of mitotic and meiotic chromosome segregation in hybrids, as documented previously. The chromosome structures detected here are still difficult to sequence and assemble, demonstrating the value of cytogenetics as a complementary approach to understand the genomic bases of speciation. © 2016 John Wiley & Sons Ltd.

Efficient statistical tests to compare Youden index: accounting for contingency correlation.

PubMed

Chen, Fangyao; Xue, Yuqiang; Tan, Ming T; Chen, Pingyan

2015-04-30

Youden index is widely utilized in studies evaluating accuracy of diagnostic tests and performance of predictive, prognostic, or risk models. However, both one and two independent sample tests on Youden index have been derived ignoring the dependence (association) between sensitivity and specificity, resulting in potentially misleading findings. Besides, paired sample test on Youden index is currently unavailable. This article develops efficient statistical inference procedures for one sample, independent, and paired sample tests on Youden index by accounting for contingency correlation, namely associations between sensitivity and specificity and paired samples typically represented in contingency tables. For one and two independent sample tests, the variances are estimated by Delta method, and the statistical inference is based on the central limit theory, which are then verified by bootstrap estimates. For paired samples test, we show that the estimated covariance of the two sensitivities and specificities can be represented as a function of kappa statistic so the test can be readily carried out. We then show the remarkable accuracy of the estimated variance using a constrained optimization approach. Simulation is performed to evaluate the statistical properties of the derived tests. The proposed approaches yield more stable type I errors at the nominal level and substantially higher power (efficiency) than does the original Youden's approach. Therefore, the simple explicit large sample solution performs very well. Because we can readily implement the asymptotic and exact bootstrap computation with common software like R, the method is broadly applicable to the evaluation of diagnostic tests and model performance. Copyright © 2015 John Wiley & Sons, Ltd.

Evidence that pairing with genetically similar mates is maladaptive in a monogamous bird

USGS Publications Warehouse

Mulard, Hervé; Danchin, E.; Talbot, S.L.; Ramey, A.M.; Hatch, Shyla A.; White, J.F.; Helfenstein, F.; Wagner, R.H.

2009-01-01

Background. Evidence of multiple genetic criteria of mate choice is accumulating in numerous taxa. In many species, females have been shown to pair with genetically dissimilar mates or with extra-pair partners that are more genetically compatible than their social mates, thereby increasing their offsprings' heterozygosity which often correlates with offspring fitness. While most studies have focused on genetically promiscuous species, few studies have addressed genetically monogamous species, in which mate choice tends to be mutual. Results. Here, we used microsatellite markers to assess individual global heterozygosity and genetic similarity of pairs in a socially and genetically monogamous seabird, the black-legged kittiwake Rissa tridactyla. We found that pairs were more genetically dissimilar than expected by chance. We also identified fitness costs of breeding with genetically similar partners: (i) genetic similarity of pairs was negatively correlated with the number of chicks hatched, and (ii) offspring heterozygosity was positively correlated with growth rate and survival. Conclusion. These findings provide evidence that breeders in a genetically monogamous species may avoid the fitness costs of reproducing with a genetically similar mate. In such species that lack the opportunity to obtain extra-pair fertilizations, mate choice may therefore be under high selective pressure. ?? 2009 Mulard et al; licensee BioMed Central Ltd.

Correlates of genetic monogamy in socially monogamous mammals: insights from Azara's owl monkeys

PubMed Central

Huck, Maren; Fernandez-Duque, Eduardo; Babb, Paul; Schurr, Theodore

2014-01-01

Understanding the evolution of mating systems, a central topic in evolutionary biology for more than 50 years, requires examining the genetic consequences of mating and the relationships between social systems and mating systems. Among pair-living mammals, where genetic monogamy is extremely rare, the extent of extra-group paternity rates has been associated with male participation in infant care, strength of the pair bond and length of the breeding season. This study evaluated the relationship between two of those factors and the genetic mating system of socially monogamous mammals, testing predictions that male care and strength of pair bond would be negatively correlated with rates of extra-pair paternity (EPP). Autosomal microsatellite analyses provide evidence for genetic monogamy in a pair-living primate with bi-parental care, the Azara's owl monkey (Aotus azarae). A phylogenetically corrected generalized least square analysis was used to relate male care and strength of the pair bond to their genetic mating system (i.e. proportions of EPP) in 15 socially monogamous mammalian species. The intensity of male care was correlated with EPP rates in mammals, while strength of pair bond failed to reach statistical significance. Our analyses show that, once social monogamy has evolved, paternal care, and potentially also close bonds, may facilitate the evolution of genetic monogamy. PMID:24648230

Correlates of genetic monogamy in socially monogamous mammals: insights from Azara's owl monkeys.

PubMed

Huck, Maren; Fernandez-Duque, Eduardo; Babb, Paul; Schurr, Theodore

2014-05-07

Understanding the evolution of mating systems, a central topic in evolutionary biology for more than 50 years, requires examining the genetic consequences of mating and the relationships between social systems and mating systems. Among pair-living mammals, where genetic monogamy is extremely rare, the extent of extra-group paternity rates has been associated with male participation in infant care, strength of the pair bond and length of the breeding season. This study evaluated the relationship between two of those factors and the genetic mating system of socially monogamous mammals, testing predictions that male care and strength of pair bond would be negatively correlated with rates of extra-pair paternity (EPP). Autosomal microsatellite analyses provide evidence for genetic monogamy in a pair-living primate with bi-parental care, the Azara's owl monkey (Aotus azarae). A phylogenetically corrected generalized least square analysis was used to relate male care and strength of the pair bond to their genetic mating system (i.e. proportions of EPP) in 15 socially monogamous mammalian species. The intensity of male care was correlated with EPP rates in mammals, while strength of pair bond failed to reach statistical significance. Our analyses show that, once social monogamy has evolved, paternal care, and potentially also close bonds, may facilitate the evolution of genetic monogamy.

The genetics of shovel shape in maxillary central incisors in man.

PubMed

Blanco, R; Chakraborty, R

1976-03-01

From dental casts of 94 parent-offspring and 127 full-sib pairs, sampled from two Chilean populations, shovelling indices are computed to measure the degree of shovelling of maxillary central incisors quantitatively. Genetic correlations are computed to determine the role of genetic factors in explaining the variation in this trait. Assuming only hereditary factors to be responsible for the transmission of shovel shape, 68% of total variability is ascribed to the additive effect of genes.

Immediate changes in spinal height and pain after aquatic vertical traction in patients with persistent low back symptoms: a crossover clinical trial.

PubMed

Simmerman, Susanne M; Sizer, Phillip S; Dedrick, Gregory S; Apte, Gail G; Brismée, Jean-Michel

2011-05-01

To investigate the effect of aquatic vertical traction on spinal height, pain intensity, and centralization response compared with a land-based supine flexion position for patients with low back pain and signs of nerve root compression. Single-blind, repeated-measures crossover design. Outpatient physical therapy clinic. Ninety-eight subjects were recruited using consecutive sampling, with 28 men and 32 women of a mean ± standard deviation (SD) age of 59.6 ± 11.6 years completing testing. Each subject participated in 2 sessions that consisted of loaded walking for 15 minutes, followed by either 15 minutes of land-based supine position or 15 minutes of aquatic vertical traction. Spinal height change, measured using a commercial stadiometer, was determined after completing loaded walking and after each intervention. The mean ± SD height change of 4.99 ± 2.88 mm after aquatic vertical traction was similar to that of 4.21 ± 2.53 mm after the land-based supine flexion (P = .0969). Paired t-test indicated that both interventions resulted in significant increased height (P < .0001). Decreases in pain after aquatic intervention (2.7 ± 2.1 cm) were significantly greater than decreases after land intervention (1.7 ± 1.7 cm; P = .0034), and centralization of symptoms was more pronounced after aquatic vertical suspension compared with the supine land-based flexion condition (P < .0001). A significant correlation between height change and both pain reduction (r = 0.39; P = .001) and centralization (r = 0.29; P = .013) was observed for the aquatic intervention only. Although both the aquatic and land interventions produced significant increases in overall spinal height, the aquatic intervention produced greater pain relief and centralization response in subjects with low back pain and signs of nerve root compression. Copyright © 2011 American Academy of Physical Medicine and Rehabilitation. Published by Elsevier Inc. All rights reserved.

The Extragalactic Lens VLBI Imaging Survey (ELVIS): Investigating galaxy cores and black holes with gravitational lens central images

NASA Astrophysics Data System (ADS)

Boyce, Edward R.

This thesis describes the Extragalactic Lens VLBI Imaging Survey (ELVIS), a search for central images in gravitational lenses. We present the first four ELVIS targets, for which we have radio VLBI observations with resolutions of a few milli-arcseconds and sensitivities of 15 - 38mJy. For PMN J1838-3427, CLASS B0739+366 and CLASS B0445+123 we have not detected any central images, but have set stringent upper limits on their flux densities. For CLASS B2319+051 we have made a tentative detection of a third radio source, which may be either a central image or radio emission from the lens galaxy. Using the upper limits on the central image flux densities, we gain new information about the matter distributions in the lens galaxies of these systems. We fit a broken power law model for the matter profile, and constrain the allowed break radii and inner index of this model. To demagnify the central images to the observed level the matter profiles must be slightly shallower than or steeper than isothermal, which is consistent with previous studies of early type galaxy profiles. The presence of a super-massive black hole weakens the constraints somewhat, but the profiles are still close to isothermal. Relative to previous work, we reduce the maximum sizes of shallow cores by factors of 2 to 3, and raise the indices of r 0( r -g central cusps by g = 0.05 - 0.35. If we take the source in B2319+051 to be a central image, then we select a narrow band of allowed break radii and inner indices, finding that a constant density core has size 150--380 pc, and a pure power law has index g = 1.5 - 1.67. Our constraints still allow sufficiently shallow profiles that some super-massive black holes may form central image pairs rather than eliminating the central image, and these image pairs may be detected with future instruments. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)

Fermion superfluid with hybridized s- and p-wave pairings

NASA Astrophysics Data System (ADS)

Zhou, LiHong; Yi, Wei; Cui, XiaoLing

2017-12-01

Ever since the pioneering work of Bardeen, Cooper and Schrieffer in the 1950s, exploring novel pairing mechanisms for fermion superfluids has become one of the central tasks in modern physics. Here, we investigate a new type of fermion superfluid with hybridized s- and p-wave pairings in an ultracold spin-1/2 Fermi gas. Its occurrence is facilitated by the co-existence of comparable s- and p-wave interactions, which is realizable in a two-component 40K Fermi gas with close-by s- and p-wave Feshbach resonances. The hybridized superfluid state is stable over a considerable parameter region on the phase diagram, and can lead to intriguing patterns of spin densities and pairing fields in momentum space. In particular, it can induce a phase-locked p-wave pairing in the fermion species that has no p-wave interactions. The hybridized nature of this novel superfluid can also be confirmed by measuring the s- and p-wave contacts, which can be extracted from the high-momentum tail of the momentum distribution of each spin component. These results enrich our knowledge of pairing superfluidity in Fermi systems, and open the avenue for achieving novel fermion superfluids with multiple partial-wave scatterings in cold atomic gases.

Comparison of clinical knowledge bases for summarization of electronic health records.

PubMed

McCoy, Allison B; Sittig, Dean F; Wright, Adam

2013-01-01

Automated summarization tools that create condition-specific displays may improve clinician efficiency. These tools require new kinds of knowledge that is difficult to obtain. We compared five problem-medication pair knowledge bases generated using four previously described knowledge base development approaches. The number of pairs in the resulting mapped knowledge bases varied widely due to differing mapping techniques from the source terminologies, ranging from 2,873 to 63,977,738 pairs. The number of overlapping pairs across knowledge bases was low, with one knowledge base having half of the pairs overlapping with another knowledge base, and most having less than a third overlapping. Further research is necessary to better evaluate the knowledge bases independently in additional settings, and to identify methods to integrate the knowledge bases.

Use of linkage mapping and centrality analysis across habitat gradients to conserve connectivity of gray wolf populations in western North America.

PubMed

Carroll, Carlos; McRae, Brad H; Brookes, Allen

2012-02-01

Centrality metrics evaluate paths between all possible pairwise combinations of sites on a landscape to rank the contribution of each site to facilitating ecological flows across the network of sites. Computational advances now allow application of centrality metrics to landscapes represented as continuous gradients of habitat quality. This avoids the binary classification of landscapes into patch and matrix required by patch-based graph analyses of connectivity. It also avoids the focus on delineating paths between individual pairs of core areas characteristic of most corridor- or linkage-mapping methods of connectivity analysis. Conservation of regional habitat connectivity has the potential to facilitate recovery of the gray wolf (Canis lupus), a species currently recolonizing portions of its historic range in the western United States. We applied 3 contrasting linkage-mapping methods (shortest path, current flow, and minimum-cost-maximum-flow) to spatial data representing wolf habitat to analyze connectivity between wolf populations in central Idaho and Yellowstone National Park (Wyoming). We then applied 3 analogous betweenness centrality metrics to analyze connectivity of wolf habitat throughout the northwestern United States and southwestern Canada to determine where it might be possible to facilitate range expansion and interpopulation dispersal. We developed software to facilitate application of centrality metrics. Shortest-path betweenness centrality identified a minimal network of linkages analogous to those identified by least-cost-path corridor mapping. Current flow and minimum-cost-maximum-flow betweenness centrality identified diffuse networks that included alternative linkages, which will allow greater flexibility in planning. Minimum-cost-maximum-flow betweenness centrality, by integrating both land cost and habitat capacity, allows connectivity to be considered within planning processes that seek to maximize species protection at minimum cost. Centrality analysis is relevant to conservation and landscape genetics at a range of spatial extents, but it may be most broadly applicable within single- and multispecies planning efforts to conserve regional habitat connectivity. ©2011 Society for Conservation Biology.

A fault-tolerant information processing concept for space vehicles.

NASA Technical Reports Server (NTRS)

Hopkins, A. L., Jr.

1971-01-01

A distributed fault-tolerant information processing system is proposed, comprising a central multiprocessor, dedicated local processors, and multiplexed input-output buses connecting them together. The processors in the multiprocessor are duplicated for error detection, which is felt to be less expensive than using coded redundancy of comparable effectiveness. Error recovery is made possible by a triplicated scratchpad memory in each processor. The main multiprocessor memory uses replicated memory for error detection and correction. Local processors use any of three conventional redundancy techniques: voting, duplex pairs with backup, and duplex pairs in independent subsystems.

Coherent exciton transport in dendrimers and continuous-time quantum walks

NASA Astrophysics Data System (ADS)

Mülken, Oliver; Bierbaum, Veronika; Blumen, Alexander

2006-03-01

We model coherent exciton transport in dendrimers by continuous-time quantum walks. For dendrimers up to the second generation the coherent transport shows perfect recurrences when the initial excitation starts at the central node. For larger dendrimers, the recurrence ceases to be perfect, a fact which resembles results for discrete quantum carpets. Moreover, depending on the initial excitation site, we find that the coherent transport to certain nodes of the dendrimer has a very low probability. When the initial excitation starts from the central node, the problem can be mapped onto a line which simplifies the computational effort. Furthermore, the long time average of the quantum mechanical transition probabilities between pairs of nodes shows characteristic patterns and allows us to classify the nodes into clusters with identical limiting probabilities. For the (space) average of the quantum mechanical probability to be still or to be again at the initial site, we obtain, based on the Cauchy-Schwarz inequality, a simple lower bound which depends only on the eigenvalue spectrum of the Hamiltonian.

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

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

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

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

PubMed Central

Yusupov, Marat; Yusupova, Gulnara

2014-01-01

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

MOLECULAR VACUUM PUMP

DOEpatents

Eckberg, E.E.

1960-09-27

A multiple molecular vacuum pump capable of producing a vacuum of the order of 10/sup -9/ mm Hg is described. The pump comprises a casing of an aggregate of paired and matched cylindrical plates, a recessed portion on one face of each plate concentrically positioned formed by a radially extending wall and matching the similarly recessed portion of its twin plate of that pair of plates and for all paired and matched plates; a plurality of grooves formed in the radially extending walls of each and all recesses progressing in a spiral manner from their respective starting points out at the periphery of the recess inwardly to the central area; a plurality of rotors rotatably mounted to closely occupy the spaces as presented by the paired and matched recesses between all paired plates; a hollowed drive-shaft perforated at points adjacent to the termini of all spiral grooves; inlet ports at the starting points of all grooves and through all plates at common points to each respectively; and a common outlet passage presented by the hollow portion of the perforated hollowed drive-shaft of the molecular pump. (AEC)

Unitary Fermi gas in a harmonic trap

NASA Astrophysics Data System (ADS)

Chang, S. Y.; Bertsch, G. F.

2007-08-01

We present an ab initio calculation of small numbers of trapped, strongly interacting fermions using the Green’s function Monte Carlo method. The ground-state energy, density profile, and pairing gap are calculated for particle numbers N=2 22 using the parameter-free “unitary” interaction. Trial wave functions are taken in the form of correlated pairs in a harmonic oscillator basis. We find that the lowest energies are obtained with a minimum explicit pair correlation beyond that needed to exploit the degeneracy of oscillator states. We find that the energies can be well fitted by the expression aTFETF+Δmod(N,2) where ETF is the Thomas-Fermi energy of a noninteracting gas in the trap and Δ is the pairing gap. There is no evidence of a shell correction energy in the systematics, but the density distributions show pronounced shell effects. We find the value Δ=0.7±0.2ω for the pairing gap. This is smaller than the value found for the uniform gas at a density corresponding to the central density of the trapped gas.

Analysis of Food Pairing in Regional Cuisines of India

PubMed Central

Bagler, Ganesh

2015-01-01

Any national cuisine is a sum total of its variety of regional cuisines, which are the cultural and historical identifiers of their respective regions. India is home to a number of regional cuisines that showcase its culinary diversity. Here, we study recipes from eight different regional cuisines of India spanning various geographies and climates. We investigate the phenomenon of food pairing which examines compatibility of two ingredients in a recipe in terms of their shared flavor compounds. Food pairing was enumerated at the level of cuisine, recipes as well as ingredient pairs by quantifying flavor sharing between pairs of ingredients. Our results indicate that each regional cuisine follows negative food pairing pattern; more the extent of flavor sharing between two ingredients, lesser their co-occurrence in that cuisine. We find that frequency of ingredient usage is central in rendering the characteristic food pairing in each of these cuisines. Spice and dairy emerged as the most significant ingredient classes responsible for the biased pattern of food pairing. Interestingly while individual spices contribute to negative food pairing, dairy products on the other hand tend to deviate food pairing towards positive side. Our data analytical study highlighting statistical properties of the regional cuisines, brings out their culinary fingerprints that could be used to design algorithms for generating novel recipes and recipe recommender systems. It forms a basis for exploring possible causal connection between diet and health as well as prospection of therapeutic molecules from food ingredients. Our study also provides insights as to how big data can change the way we look at food. PMID:26430895

Analysis of Food Pairing in Regional Cuisines of India.

PubMed

Jain, Anupam; N K, Rakhi; Bagler, Ganesh

2015-01-01

Any national cuisine is a sum total of its variety of regional cuisines, which are the cultural and historical identifiers of their respective regions. India is home to a number of regional cuisines that showcase its culinary diversity. Here, we study recipes from eight different regional cuisines of India spanning various geographies and climates. We investigate the phenomenon of food pairing which examines compatibility of two ingredients in a recipe in terms of their shared flavor compounds. Food pairing was enumerated at the level of cuisine, recipes as well as ingredient pairs by quantifying flavor sharing between pairs of ingredients. Our results indicate that each regional cuisine follows negative food pairing pattern; more the extent of flavor sharing between two ingredients, lesser their co-occurrence in that cuisine. We find that frequency of ingredient usage is central in rendering the characteristic food pairing in each of these cuisines. Spice and dairy emerged as the most significant ingredient classes responsible for the biased pattern of food pairing. Interestingly while individual spices contribute to negative food pairing, dairy products on the other hand tend to deviate food pairing towards positive side. Our data analytical study highlighting statistical properties of the regional cuisines, brings out their culinary fingerprints that could be used to design algorithms for generating novel recipes and recipe recommender systems. It forms a basis for exploring possible causal connection between diet and health as well as prospection of therapeutic molecules from food ingredients. Our study also provides insights as to how big data can change the way we look at food.

J/ψ suppression at forward rapidity in Pb-Pb collisions at √{sNN} = 5.02 TeV

NASA Astrophysics Data System (ADS)

Adam, J.; Adamová, D.; Aggarwal, M. M.; Aglieri Rinella, G.; Agnello, M.; Agrawal, N.; Ahammed, Z.; Ahmad, S.; Ahn, S. U.; Aiola, S.; Akindinov, A.; Alam, S. N.; Albuquerque, D. S. D.; Aleksandrov, D.; Alessandro, B.; Alexandre, D.; Alfaro Molina, R.; Alici, A.; Alkin, A.; Alme, J.; Alt, T.; Altinpinar, S.; Altsybeev, I.; Alves Garcia Prado, C.; An, M.; Andrei, C.; Andrews, H. A.; Andronic, A.; Anguelov, V.; Anson, C.; Antičić, T.; Antinori, F.; Antonioli, P.; Aphecetche, L.; Appelshäuser, H.; Arcelli, S.; Arnaldi, R.; Arnold, O. W.; Arsene, I. C.; Arslandok, M.; Audurier, B.; Augustinus, A.; Averbeck, R.; Azmi, M. D.; Badalà, A.; Baek, Y. W.; Bagnasco, S.; Bailhache, R.; Bala, R.; Balasubramanian, S.; Baldisseri, A.; Baral, R. C.; Barbano, A. M.; Barbera, R.; Barile, F.; Barnaföldi, G. G.; Barnby, L. S.; Barret, V.; Bartalini, P.; Barth, K.; Bartke, J.; Bartsch, E.; Basile, M.; Bastid, N.; Basu, S.; Bathen, B.; Batigne, G.; Batista Camejo, A.; Batyunya, B.; Batzing, P. C.; Bearden, I. G.; Beck, H.; Bedda, C.; Behera, N. K.; Belikov, I.; Bellini, F.; Bello Martinez, H.; Bellwied, R.; Belmont, R.; Belmont-Moreno, E.; Beltran, L. G. E.; Belyaev, V.; Bencedi, G.; Beole, S.; Berceanu, I.; Bercuci, A.; Berdnikov, Y.; Berenyi, D.; Bertens, R. A.; Berzano, D.; Betev, L.; Bhasin, A.; Bhat, I. R.; Bhati, A. K.; Bhattacharjee, B.; Bhom, J.; Bianchi, L.; Bianchi, N.; Bianchin, C.; Bielčík, J.; Bielčíková, J.; Bilandzic, A.; Biro, G.; Biswas, R.; Biswas, S.; Bjelogrlic, S.; Blair, J. T.; Blau, D.; Blume, C.; Bock, F.; Bogdanov, A.; Bøggild, H.; Boldizsár, L.; Bombara, M.; Bonora, M.; Book, J.; Borel, H.; Borissov, A.; Borri, M.; Bossú, F.; Botta, E.; Bourjau, C.; Braun-Munzinger, P.; Bregant, M.; Breitner, T.; Broker, T. A.; Browning, T. A.; Broz, M.; Brucken, E. J.; Bruna, E.; Bruno, G. E.; Budnikov, D.; Buesching, H.; Bufalino, S.; Buitron, S. A. I.; Buncic, P.; Busch, O.; Buthelezi, Z.; Butt, J. B.; Buxton, J. T.; Cabala, J.; Caffarri, D.; Cai, X.; Caines, H.; Calero Diaz, L.; Caliva, A.; Calvo Villar, E.; Camerini, P.; Carena, F.; Carena, W.; Carnesecchi, F.; Castillo Castellanos, J.; Castro, A. J.; Casula, E. A. R.; Ceballos Sanchez, C.; Cepila, J.; Cerello, P.; Cerkala, J.; Chang, B.; Chapeland, S.; Chartier, M.; Charvet, J. L.; Chattopadhyay, S.; Chattopadhyay, S.; Chauvin, A.; Chelnokov, V.; Cherney, M.; Cheshkov, C.; Cheynis, B.; Chibante Barroso, V.; Chinellato, D. D.; Cho, S.; Chochula, P.; Choi, K.; Chojnacki, M.; Choudhury, S.; Christakoglou, P.; Christensen, C. H.; Christiansen, P.; Chujo, T.; Chung, S. U.; Cicalo, C.; Cifarelli, L.; Cindolo, F.; Cleymans, J.; Colamaria, F.; Colella, D.; Collu, A.; Colocci, M.; Conesa Balbastre, G.; Conesa Del Valle, Z.; Connors, M. E.; Contreras, J. G.; Cormier, T. M.; Corrales Morales, Y.; Cortés Maldonado, I.; Cortese, P.; Cosentino, M. R.; Costa, F.; Crkovská, J.; Crochet, P.; Cruz Albino, R.; Cuautle, E.; Cunqueiro, L.; Dahms, T.; Dainese, A.; Danisch, M. C.; Danu, A.; Das, D.; Das, I.; Das, S.; Dash, A.; Dash, S.; de, S.; de Caro, A.; de Cataldo, G.; de Conti, C.; de Cuveland, J.; de Falco, A.; de Gruttola, D.; De Marco, N.; de Pasquale, S.; de Souza, R. D.; Deisting, A.; Deloff, A.; Deplano, C.; Dhankher, P.; di Bari, D.; di Mauro, A.; di Nezza, P.; di Ruzza, B.; Diaz Corchero, M. A.; Dietel, T.; Dillenseger, P.; Divià, R.; Djuvsland, Ø.; Dobrin, A.; Domenicis Gimenez, D.; Dönigus, B.; Dordic, O.; Drozhzhova, T.; Dubey, A. K.; Dubla, A.; Ducroux, L.; Dupieux, P.; Ehlers, R. J.; Elia, D.; Endress, E.; Engel, H.; Epple, E.; Erazmus, B.; Erdemir, I.; Erhardt, F.; Espagnon, B.; Estienne, M.; Esumi, S.; Eulisse, G.; Eum, J.; Evans, D.; Evdokimov, S.; Eyyubova, G.; Fabbietti, L.; Fabris, D.; Faivre, J.; Fantoni, A.; Fasel, M.; Feldkamp, L.; Feliciello, A.; Feofilov, G.; Ferencei, J.; Fernández Téllez, A.; Ferreiro, E. G.; Ferretti, A.; Festanti, A.; Feuillard, V. J. G.; Figiel, J.; Figueredo, M. A. S.; Filchagin, S.; Finogeev, D.; Fionda, F. M.; Fiore, E. M.; Floris, M.; Foertsch, S.; Foka, P.; Fokin, S.; Fragiacomo, E.; Francescon, A.; Francisco, A.; Frankenfeld, U.; Fronze, G. G.; Fuchs, U.; Furget, C.; Furs, A.; Fusco Girard, M.; Gaardhøje, J. J.; Gagliardi, M.; Gago, A. M.; Gajdosova, K.; Gallio, M.; Galvan, C. D.; Gangadharan, D. R.; Ganoti, P.; Gao, C.; Garabatos, C.; Garcia-Solis, E.; Garg, K.; Gargiulo, C.; Gasik, P.; Gauger, E. F.; Germain, M.; Gheata, M.; Ghosh, P.; Ghosh, S. K.; Gianotti, P.; Giubellino, P.; Giubilato, P.; Gladysz-Dziadus, E.; Glässel, P.; Goméz Coral, D. M.; Gomez Ramirez, A.; Gonzalez, A. S.; Gonzalez, V.; González-Zamora, P.; Gorbunov, S.; Görlich, L.; Gotovac, S.; Grabski, V.; Grachov, O. A.; Graczykowski, L. K.; Graham, K. L.; Grelli, A.; Grigoras, A.; Grigoras, C.; Grigoriev, V.; Grigoryan, A.; Grigoryan, S.; Grinyov, B.; Grion, N.; Gronefeld, J. M.; Grosse-Oetringhaus, J. F.; Grosso, R.; Gruber, L.; Guber, F.; Guernane, R.; Guerzoni, B.; Gulbrandsen, K.; Gunji, T.; Gupta, A.; Gupta, R.; Guzman, I. B.; Haake, R.; Hadjidakis, C.; Haiduc, M.; Hamagaki, H.; Hamar, G.; Hamon, J. C.; Harris, J. W.; Harton, A.; Hatzifotiadou, D.; Hayashi, S.; Heckel, S. T.; Hellbär, E.; Helstrup, H.; Herghelegiu, A.; Herrera Corral, G.; Herrmann, F.; Hess, B. A.; Hetland, K. F.; Hillemanns, H.; Hippolyte, B.; Horak, D.; Hosokawa, R.; Hristov, P.; Hughes, C.; Humanic, T. J.; Hussain, N.; Hussain, T.; Hutter, D.; Hwang, D. S.; Ilkaev, R.; Inaba, M.; Incani, E.; Ippolitov, M.; Irfan, M.; Isakov, V.; Ivanov, M.; Ivanov, V.; Izucheev, V.; Jacak, B.; Jacazio, N.; Jacobs, P. M.; Jadhav, M. B.; Jadlovska, S.; Jadlovsky, J.; Jahnke, C.; Jakubowska, M. J.; Janik, M. A.; Jayarathna, P. H. S. Y.; Jena, C.; Jena, S.; Jimenez Bustamante, R. T.; Jones, P. G.; Jung, H.; Jusko, A.; Kalinak, P.; Kalweit, A.; Kang, J. H.; Kaplin, V.; Kar, S.; Karasu Uysal, A.; Karavichev, O.; Karavicheva, T.; Karayan, L.; Karpechev, E.; Kebschull, U.; Keidel, R.; Keijdener, D. L. D.; Keil, M.; Mohisin Khan, M.; Khan, P.; Khan, S. A.; Khanzadeev, A.; Kharlov, Y.; Khatun, A.; Kileng, B.; Kim, D. W.; Kim, D. J.; Kim, D.; Kim, H.; Kim, J. S.; Kim, J.; Kim, M.; Kim, M.; Kim, S.; Kim, T.; Kirsch, S.; Kisel, I.; Kiselev, S.; Kisiel, A.; Kiss, G.; Klay, J. L.; Klein, C.; Klein, J.; Klein-Bösing, C.; Klewin, S.; Kluge, A.; Knichel, M. L.; Knospe, A. G.; Kobdaj, C.; Kofarago, M.; Kollegger, T.; Kolojvari, A.; Kondratiev, V.; Kondratyeva, N.; Kondratyuk, E.; Konevskikh, A.; Kopcik, M.; Kour, M.; Kouzinopoulos, C.; Kovalenko, O.; Kovalenko, V.; Kowalski, M.; Koyithatta Meethaleveedu, G.; Králik, I.; Kravčáková, A.; Krivda, M.; Krizek, F.; Kryshen, E.; Krzewicki, M.; Kubera, A. M.; Kučera, V.; Kuhn, C.; Kuijer, P. G.; Kumar, A.; Kumar, J.; Kumar, L.; Kumar, S.; Kurashvili, P.; Kurepin, A.; Kurepin, A. B.; Kuryakin, A.; Kweon, M. J.; Kwon, Y.; La Pointe, S. L.; La Rocca, P.; Ladron de Guevara, P.; Lagana Fernandes, C.; Lakomov, I.; Langoy, R.; Lapidus, K.; Lara, C.; Lardeux, A.; Lattuca, A.; Laudi, E.; Lea, R.; Leardini, L.; Lee, S.; Lehas, F.; Lehner, S.; Lemmon, R. C.; Lenti, V.; Leogrande, E.; León Monzón, I.; León Vargas, H.; Leoncino, M.; Lévai, P.; Li, S.; Li, X.; Lien, J.; Lietava, R.; Lindal, S.; Lindenstruth, V.; Lippmann, C.; Lisa, M. A.; Ljunggren, H. M.; Lodato, D. F.; Loenne, P. I.; Loginov, V.; Loizides, C.; Lopez, X.; López Torres, E.; Lowe, A.; Luettig, P.; Lunardon, M.; Luparello, G.; Lupi, M.; Lutz, T. H.; Maevskaya, A.; Mager, M.; Mahajan, S.; Mahmood, S. M.; Maire, A.; Majka, R. D.; Malaev, M.; Maldonado Cervantes, I.; Malinina, L.; Mal'Kevich, D.; Malzacher, P.; Mamonov, A.; Manko, V.; Manso, F.; Manzari, V.; Mao, Y.; Marchisone, M.; Mareš, J.; Margagliotti, G. V.; Margotti, A.; Margutti, J.; Marín, A.; Markert, C.; Marquard, M.; Martin, N. A.; Martinengo, P.; Martínez, M. I.; Martínez García, G.; Martinez Pedreira, M.; Mas, A.; Masciocchi, S.; Masera, M.; Masoni, A.; Mastroserio, A.; Matyja, A.; Mayer, C.; Mazer, J.; Mazzilli, M.; Mazzoni, M. A.; Meddi, F.; Melikyan, Y.; Menchaca-Rocha, A.; Meninno, E.; Mercado Pérez, J.; Meres, M.; Mhlanga, S.; Miake, Y.; Mieskolainen, M. M.; Mikhaylov, K.; Milano, L.; Milosevic, J.; Mischke, A.; Mishra, A. N.; Mishra, T.; Miśkowiec, D.; Mitra, J.; Mitu, C. M.; Mohammadi, N.; Mohanty, B.; Molnar, L.; Montaño Zetina, L.; Montes, E.; Moreira de Godoy, D. A.; Moreno, L. A. P.; Moretto, S.; Morreale, A.; Morsch, A.; Muccifora, V.; Mudnic, E.; Mühlheim, D.; Muhuri, S.; Mukherjee, M.; Mulligan, J. D.; Munhoz, M. G.; Münning, K.; Munzer, R. H.; Murakami, H.; Murray, S.; Musa, L.; Musinsky, J.; Naik, B.; Nair, R.; Nandi, B. K.; Nania, R.; Nappi, E.; Naru, M. U.; Natal da Luz, H.; Nattrass, C.; Navarro, S. R.; Nayak, K.; Nayak, R.; Nayak, T. K.; Nazarenko, S.; Nedosekin, A.; Negrao de Oliveira, R. A.; Nellen, L.; Ng, F.; Nicassio, M.; Niculescu, M.; Niedziela, J.; Nielsen, B. S.; Nikolaev, S.; Nikulin, S.; Nikulin, V.; Noferini, F.; Nomokonov, P.; Nooren, G.; Noris, J. C. C.; Norman, J.; Nyanin, A.; Nystrand, J.; Oeschler, H.; Oh, S.; Oh, S. K.; Ohlson, A.; Okatan, A.; Okubo, T.; Olah, L.; Oleniacz, J.; Oliveira da Silva, A. C.; Oliver, M. H.; Onderwaater, J.; Oppedisano, C.; Orava, R.; Oravec, M.; Ortiz Velasquez, A.; Oskarsson, A.; Otwinowski, J.; Oyama, K.; Ozdemir, M.; Pachmayer, Y.; Pagano, D.; Pagano, P.; Paić, G.; Pal, S. K.; Palni, P.; Pan, J.; Pandey, A. K.; Papikyan, V.; Pappalardo, G. S.; Pareek, P.; Park, J.; Park, W. J.; Parmar, S.; Passfeld, A.; Paticchio, V.; Patra, R. N.; Paul, B.; Pei, H.; Peitzmann, T.; Peng, X.; Pereira da Costa, H.; Peresunko, D.; Perez Lezama, E.; Peskov, V.; Pestov, Y.; Petráček, V.; Petrov, V.; Petrovici, M.; Petta, C.; Piano, S.; Pikna, M.; Pillot, P.; Pimentel, L. O. D. L.; Pinazza, O.; Pinsky, L.; Piyarathna, D. B.; Płoskoń, M.; Planinic, M.; Pluta, J.; Pochybova, S.; Podesta-Lerma, P. L. M.; Poghosyan, M. G.; Polichtchouk, B.; Poljak, N.; Poonsawat, W.; Pop, A.; Poppenborg, H.; Porteboeuf-Houssais, S.; Porter, J.; Pospisil, J.; Prasad, S. K.; Preghenella, R.; Prino, F.; Pruneau, C. A.; Pshenichnov, I.; Puccio, M.; Puddu, G.; Pujahari, P.; Punin, V.; Putschke, J.; Qvigstad, H.; Rachevski, A.; Raha, S.; Rajput, S.; Rak, J.; Rakotozafindrabe, A.; Ramello, L.; Rami, F.; Raniwala, R.; Raniwala, S.; Räsänen, S. S.; Rascanu, B. T.; Rathee, D.; Ratza, V.; Ravasenga, I.; Read, K. F.; Redlich, K.; Reed, R. J.; Rehman, A.; Reichelt, P.; Reidt, F.; Ren, X.; Renfordt, R.; Reolon, A. R.; Reshetin, A.; Reygers, K.; Riabov, V.; Ricci, R. A.; Richert, T.; Richter, M.; Riedler, P.; Riegler, W.; Riggi, F.; Ristea, C.; Rodríguez Cahuantzi, M.; Rodriguez Manso, A.; Røed, K.; Rogochaya, E.; Rohr, D.; Röhrich, D.; Ronchetti, F.; Ronflette, L.; Rosnet, P.; Rossi, A.; Roukoutakis, F.; Roy, A.; Roy, C.; Roy, P.; Rubio Montero, A. J.; Rui, R.; Russo, R.; Ryabinkin, E.; Ryabov, Y.; Rybicki, A.; Saarinen, S.; Sadhu, S.; Sadovsky, S.; Šafařík, K.; Sahlmuller, B.; Sahoo, P.; Sahoo, R.; Sahoo, S.; Sahu, P. K.; Saini, J.; Sakai, S.; Saleh, M. A.; Salzwedel, J.; Sambyal, S.; Samsonov, V.; Šándor, L.; Sandoval, A.; Sano, M.; Sarkar, D.; Sarkar, N.; Sarma, P.; Scapparone, E.; Scarlassara, F.; Schiaua, C.; Schicker, R.; Schmidt, C.; Schmidt, H. R.; Schmidt, M.; Schuchmann, S.; Schukraft, J.; Schutz, Y.; Schwarz, K.; Schweda, K.; Scioli, G.; Scomparin, E.; Scott, R.; Šefčík, M.; Seger, J. E.; Sekiguchi, Y.; Sekihata, D.; Selyuzhenkov, I.; Senosi, K.; Senyukov, S.; Serradilla, E.; Sevcenco, A.; Shabanov, A.; Shabetai, A.; Shadura, O.; Shahoyan, R.; Shangaraev, A.; Sharma, A.; Sharma, M.; Sharma, M.; Sharma, N.; Sheikh, A. I.; Shigaki, K.; Shou, Q.; Shtejer, K.; Sibiriak, Y.; Siddhanta, S.; Sielewicz, K. M.; Siemiarczuk, T.; Silvermyr, D.; Silvestre, C.; Simatovic, G.; Simonetti, G.; Singaraju, R.; Singh, R.; Singhal, V.; Sinha, T.; Sitar, B.; Sitta, M.; Skaali, T. B.; Slupecki, M.; Smirnov, N.; Snellings, R. J. M.; Snellman, T. W.; Song, J.; Song, M.; Song, Z.; Soramel, F.; Sorensen, S.; Sozzi, F.; Spiriti, E.; Sputowska, I.; Spyropoulou-Stassinaki, M.; Stachel, J.; Stan, I.; Stankus, P.; Stenlund, E.; Steyn, G.; Stiller, J. H.; Stocco, D.; Strmen, P.; Suaide, A. A. P.; Sugitate, T.; Suire, C.; Suleymanov, M.; Suljic, M.; Sultanov, R.; Šumbera, M.; Sumowidagdo, S.; Swain, S.; Szabo, A.; Szarka, I.; Szczepankiewicz, A.; Szymanski, M.; Tabassam, U.; Takahashi, J.; Tambave, G. J.; Tanaka, N.; Tarhini, M.; Tariq, M.; Tarzila, M. G.; Tauro, A.; Tejeda Muñoz, G.; Telesca, A.; Terasaki, K.; Terrevoli, C.; Teyssier, B.; Thäder, J.; Thakur, D.; Thomas, D.; Tieulent, R.; Tikhonov, A.; Timmins, A. R.; Toia, A.; Trogolo, S.; Trombetta, G.; Trubnikov, V.; Trzaska, W. H.; Tsuji, T.; Tumkin, A.; Turrisi, R.; Tveter, T. S.; Ullaland, K.; Uras, A.; Usai, G. L.; Utrobicic, A.; Vala, M.; Valencia Palomo, L.; van der Maarel, J.; van Hoorne, J. W.; van Leeuwen, M.; Vanat, T.; Vande Vyvre, P.; Varga, D.; Vargas, A.; Vargyas, M.; Varma, R.; Vasileiou, M.; Vasiliev, A.; Vauthier, A.; Vázquez Doce, O.; Vechernin, V.; Veen, A. M.; Velure, A.; Vercellin, E.; Vergara Limón, S.; Vernet, R.; Vickovic, L.; Viinikainen, J.; Vilakazi, Z.; Villalobos Baillie, O.; Villatoro Tello, A.; Vinogradov, A.; Vinogradov, L.; Virgili, T.; Vislavicius, V.; Viyogi, Y. P.; Vodopyanov, A.; Völkl, M. A.; Voloshin, K.; Voloshin, S. A.; Volpe, G.; von Haller, B.; Vorobyev, I.; Vranic, D.; Vrláková, J.; Vulpescu, B.; Wagner, B.; Wagner, J.; Wang, H.; Wang, M.; Watanabe, D.; Watanabe, Y.; Weber, M.; Weber, S. G.; Weiser, D. F.; Wessels, J. P.; Westerhoff, U.; Whitehead, A. M.; Wiechula, J.; Wikne, J.; Wilk, G.; Wilkinson, J.; Willems, G. A.; Williams, M. C. S.; Windelband, B.; Winn, M.; Yalcin, S.; Yang, P.; Yano, S.; Yin, Z.; Yokoyama, H.; Yoo, I.-K.; Yoon, J. H.; Yurchenko, V.; Zaccolo, V.; Zaman, A.; Zampolli, C.; Zanoli, H. J. C.; Zaporozhets, S.; Zardoshti, N.; Zarochentsev, A.; Závada, P.; Zaviyalov, N.; Zbroszczyk, H.; Zgura, I. S.; Zhalov, M.; Zhang, H.; Zhang, X.; Zhang, Y.; Zhang, C.; Zhang, Z.; Zhao, C.; Zhigareva, N.; Zhou, D.; Zhou, Y.; Zhou, Z.; Zhu, H.; Zhu, J.; Zichichi, A.; Zimmermann, A.; Zimmermann, M. B.; Zinovjev, G.; Zyzak, M.; Alice Collaboration

2017-03-01

The inclusive J/ψ production has been studied in Pb-Pb and pp collisions at the centre-of-mass energy per nucleon pair √{sNN} = 5.02 TeV, using the ALICE detector at the CERN LHC. The J/ψ meson is reconstructed, in the centre-of-mass rapidity interval 2.5 < y < 4 and in the transverse-momentum range pT < 12 GeV / c, via its decay to a muon pair. In this Letter, we present results on the inclusive J/ψ cross section in pp collisions at √{ s} = 5.02 TeV and on the nuclear modification factor RAA. The latter is presented as a function of the centrality of the collision and, for central collisions, as a function of the transverse momentum pT of the J/ψ. The measured RAA values indicate a suppression of the J/ψ in nuclear collisions and are then compared to our previous results obtained in Pb-Pb collisions at √{sNN} = 2.76 TeV. The ratio of the RAA values at the two energies is also computed and compared to calculations of statistical and dynamical models. The numerical value of the ratio for central events (0-10% centrality) is 1.17 ± 0.04 (stat) ± 0.20 (syst). In central events, as a function of pT, a slight increase of RAA with collision energy is visible in the region 2

J/ ψ suppression at forward rapidity in Pb–Pb collisions at s NN = 5.02  TeV

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

Adam, J.; Adamová, D.; Aggarwal, M. M.

Tmore » he inclusive J/ψ production has been studied in Pb–Pb and pp collisions at the centre-of-mass energy per nucleon pair s NN = 5.02  eV , using the ALICE detector at the CERN LHC. he J/ψ meson is reconstructed, in the centre-of-mass rapidity interval 2.5 < y < 4 and in the transverse-momentum range p < 12 GeV/c, via its decay to a muon pair. In this Letter, we present results on the inclusive J/ψ cross section in pp collisions at √s = 5.02 eV and on the nuclear modification factor R AA. he latter is presented as a function of the centrality of the collision and, for central collisions, as a function of the transverse momentum p of the J/ψ. he measured R AA values indicate a suppression of the J/ψ in nuclear collisions and are then compared to our previous results obtained in Pb–Pb collisions at s NN = 2.76  eV . he ratio of the R AA values at the two energies is also computed and compared to calculations of statistical and dynamical models. he numerical value of the ratio for central events (0–10% centrality) is 1.17 ± 0.04(stat) ± 0.20(syst). In central events, as a function of p , a slight increase of R AA with collision energy is visible in the region 2 < p < 6 GeV/c. heoretical calculations qualitatively describe the measurements, within uncertainties.« less

CENTRAL REINFORCING EFFECTS OF ETHANOL ARE BLOCKED BY CATALASE INHIBITION

PubMed Central

Nizhnikov, Michael Edward; Molina, Juan Carlos; Spear, Norman

2007-01-01

Recent studies have systematically indicated that newborn rats are highly sensitive to ethanol’s positive reinforcing effects. Central administrations of ethanol (25–200 mg %) associated with an olfactory conditioned stimulus (CS) promote subsequent conditioned approach to the CS as evaluated through the newborn’s response to a surrogate nipple scented with the CS. It has been shown that ethanol’s first metabolite, acetaldehyde, exerts significant reinforcing effects in the central nervous system. A significant amount of acetaldehyde is derived from ethanol metabolism via the catalase system. In newborn rats catalase levels are particularly high in several brain structures. The present study tested the effect of catalase inhibition on central ethanol reinforcement. In the first experiment, pups experienced lemon odor either paired or unpaired with intracisternal (i.c.) administrations of 100 mg% ethanol. Half of the animals corresponding to each learning condition were pretreated with i.c. administrations of either physiological saline or a catalase inhibitor (sodium-azide). Catalase inhibition completely suppressed ethanol reinforcement in paired groups without affecting responsiveness to the CS during conditioning or responding by unpaired control groups. A second experiment tested whether these effects were specific to ethanol reinforcement or due instead to general impairment in learning and expression capabilities. Central administration of an endogenous kappa opioid receptor agonist (dynorphin A-13) was employed as an alternative source of reinforcement. Inhibition of the catalase system had no effect on the reinforcing properties of dynorphin. The present results support the hypothesis that ethanol metabolism regulated by the catalase system plays a critical role in determination of ethanol reinforcement in newborn rats. PMID:17980789

J/ ψ suppression at forward rapidity in Pb–Pb collisions at s NN = 5.02  TeV

DOE PAGES

Adam, J.; Adamová, D.; Aggarwal, M. M.; ...

2017-01-10

Tmore » he inclusive J/ψ production has been studied in Pb–Pb and pp collisions at the centre-of-mass energy per nucleon pair s NN = 5.02  eV , using the ALICE detector at the CERN LHC. he J/ψ meson is reconstructed, in the centre-of-mass rapidity interval 2.5 < y < 4 and in the transverse-momentum range p < 12 GeV/c, via its decay to a muon pair. In this Letter, we present results on the inclusive J/ψ cross section in pp collisions at √s = 5.02 eV and on the nuclear modification factor R AA. he latter is presented as a function of the centrality of the collision and, for central collisions, as a function of the transverse momentum p of the J/ψ. he measured R AA values indicate a suppression of the J/ψ in nuclear collisions and are then compared to our previous results obtained in Pb–Pb collisions at s NN = 2.76  eV . he ratio of the R AA values at the two energies is also computed and compared to calculations of statistical and dynamical models. he numerical value of the ratio for central events (0–10% centrality) is 1.17 ± 0.04(stat) ± 0.20(syst). In central events, as a function of p , a slight increase of R AA with collision energy is visible in the region 2 < p < 6 GeV/c. heoretical calculations qualitatively describe the measurements, within uncertainties.« less

Confocal microscopy refines generic concept of a problematic taxon: rediagnosis of the genus Neoprothrix and remarks on female anatomy of eriophyoids (Acari: Eriophyoidea).

PubMed

Chetverikov, Philipp E; Desnitskiy, Alexey G; Navia, Denise

2015-02-16

Due to the higher resolution, confocal microscopy (CLSM) can be applied to refine the origin of tiny structures of the autofluorescent exoskeletons of microarthropods (mites in particular) which are hard to visualize using traditional differential interference contract light microscopy (DIC LM) and phase contrast light microscopy (PC LM). Three-dimensional (3D) reconstructions of the prodorsal shield topography of eriophyoid mites using Neoprothrix hibiscus Reis and Navia as a model, suggest that the structures originally treated as paired setae vi are two internal rod-like apodemes. Based on this, the genus Neoprothrix is excluded from the subfamily Prothricinae Amrine and transferred to the subfamily Sierraphytoptinae Keifer. Observations on partially cleared specimens of N. hibiscus showed that remnants of the central nervous system, paired glands and developing oocytes can be visualized using DIC LM and CLSM methods. New high quality microscope images are provided of recently described "flower-shaped" structures and two main components of yolk inclusions of the mature eggs inside the oviduct.

Molecular identification and description of the female of Nothoaspis reddelli (Ixodida: Argasidae) from a cave in southeastern Mexico.

PubMed

Guzmán-Cornejo, Carmen; Paredes-León, Ricardo; Labruna, Marcelo B; Nava, Santiago; Venzal, José M

2012-10-01

Nothoaspis reddelli Keirans and Clifford, 1975 , was described from 3 males collected in Grutas de Xtacumbilxunaán, Campeche, Mexico, although females have remained undescribed for 37 yr. Recently adult females of this species were collected from Cueva de Villa Luz ( =  Cueva de las Sardinas, Cueva del Azufre), in Tapijulapa, Tabasco, Mexico. Here we present a morphological description of the female stage, together with 16S rDNA sequences that confirm the conspecificity of our female, male, and nymphal specimens. The female integument of the anterior portion of the dorsal surface is smooth (nothoaspis), appearing to consist of 3 large "subunits," 1 anterior and 2 posterior, each with a small sublateral "subunit" on either side. The remaining dorsal covered integument is a cell-like configuration. The hood is large and bluntly rounded, and visible dorsally. The spiracular plate is oval. It possesses 1 pair of posthypostomal setae. The palpal trochanter has 1 pair of setae and a 5/5 hypostome decreasing to 4/4 at the apex. There is a single central pore at the base of the hypostome.

A new probable stem lineage crustacean with three-dimensionally preserved soft parts from the Herefordshire (Silurian) Lagerstätte, UK

PubMed Central

Siveter, Derek J; Sutton, Mark D; Briggs, Derek E.G; Siveter, David J

2007-01-01

A new arthropod with three-dimensionally preserved soft parts, Tanazios dokeron, is described from the Wenlock Series (Silurian) of Herefordshire, England, UK. Serial grinding, digital photographic and computer rendering techniques yielded ‘virtual fossils’ in the round for study. The body tagmata of T. dokeron comprise a head shield and a long trunk. The head shield bears six pairs of horn-like spines and the head bears five pairs of appendages. The antennule, antenna and mandible are all uniramous, and the mandible includes a gnathobasic coxa. Appendages four and five are biramous and similar to those of the trunk: each comprises a limb base with an endite, an enditic membrane, and two epipodites, plus an endopod and exopod. The hypostome bears a large cone-like projection centrally, and there may be a short labrum. The trunk has some 64 segments and at least 60 appendage pairs. A very small telson has the anus sited ventrally in its posterior part and also bears a caudal furca. Comparative morphological and cladistic analyses of T. dokeron indicate a crustacean affinity, with a probable position in the eucrustacean stem group. As such the epipodites in T. dokeron are the first recorded in a eucrustacean stem taxon. The new species is interpreted as a benthic or nektobenthic scavenger. PMID:17609185

Banding patterns and chromosomal evolution in five species of neotropical Teiinae lizards (Squamata: Teiidae).

PubMed

dos Santos, Rodrigo Marques Lima; Pellegrino, Katia Cristina Machado; Rodrigues, Miguel Trefaut; Yonenaga-Yassuda, Yatiyo

2007-11-01

Karyotypes of five species of South American teiid lizards from subfamily Teiinae: Ameiva ameiva, Kentropyx calcarata, K. paulensis, K. vanzoi (2n = 50, all acrocentric), and Cnemidophorus ocellifer (2n = 50, all biarmed), are herein described and compared on the basis of conventional and silver staining, and CBG and RBG banding patterns. Meiotic data are also included. Karyotypes of K. paulensis, K. vanzoi, and C. ocellifer are reported here for the first time. Inter-generic variability in Ag-NORs location was detected with NORs occurring at the end of long arm of pair 1 in K. calcarata, K. paulensis, and K. vanzoi; pair 5 in C. ocellifer and pair 7 in A. ameiva. The location of NORs, along with the karyological differences between A. ameiva and the Central American species (A. auberi), corroboretes the molecular-based hypothesis that the genus Ameiva is paraphyletic. Inter-populational heteromorphism in Ag-NORs size was detected between populations of C. ocellifer. RBG and CBG banding data demonstrated that the biarmed condition of the C. ocellifer chromosomes is due to multiple pericentric inversion events instead of addition of constitutive heterochromatin. Differential-staining techniques used here revealed valuable information about Teiinae karyotypic diversity and made it possible to compare these species, contributing to both the better comprehension of their chromosomal evolution and issues on taxa systematics.

Observation of proton-tagged, central (semi)exclusive production of high-mass lepton pairs in pp collisions at 13 TeV with the CMS-TOTEM precision proton spectrometer

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

Sirunyan, Albert M; et al.

The process ppmore » $$\\to\\ell^+\\ell^-$$p$$^{(*)}$$, with $$\\ell^+\\ell^-$$ a muon or an electron pair produced at midrapidity with mass larger than 110 GeV, has been observed for the first time at the LHC in pp collisions at $$\\sqrt{s} =$$ 13 TeV. One of the two scattered protons is measured in the CMS-TOTEM precision proton spectrometer (CT-PPS), which operated for the first time in 2016. The second proton either remains intact or is excited and then dissociates into a low-mass state p$$^{*}$$, which is undetected. The measurement is based on an integrated luminosity of 9.4 fb$$^{-1}$$ collected during standard, high-luminosity LHC operation. A total of 12 $$\\mu^+\\mu^-$$ and 8 e$^+$e$^-$ pairs with $$m(\\ell^{+}\\ell^{-}) >$$ 110 GeV, and matching forward proton kinematics, are observed, with expected backgrounds of 1.49 $$\\pm$$ 0.07 (stat) $$\\pm$$ 0.53 (syst) and 2.36 $$\\pm$$ 0.09 (stat) $$\\pm$$ 0.47 (syst), respectively. This corresponds to an excess of more than five standard deviations over the expected background. The present result constitutes the first observation of proton-tagged $$\\gamma\\gamma$$ collisions at the electroweak scale. This measurement also demonstrates that CT-PPS performs according to the design specifications.« less

Fuel cell with electrolyte feed system

DOEpatents

Feigenbaum, Haim

1984-01-01

A fuel cell having a pair of electrodes at the sites of electrochemical reactions of hydrogen and oxygen and a phosphoric acid electrolyte provided with an electrolyte supporting structure in the form of a laminated matrix assembly disposed between the electrodes. The matrix assembly is formed of a central layer disposed between two outer layers, each being permeable to the flow of the electrolyte. The central layer is provided with relatively large pores while the outer layers are provided with relatively small pores. An external reservoir supplies electrolyte via a feed means to the central layer to compensate for changes in electrolyte volume in the matrix assembly during the operation of fuel cell.

SPARK GAP SWITCH

DOEpatents

Neal, R.B.

1957-12-17

An improved triggered spark gap switch is described, capable of precisely controllable firing time while switching very large amounts of power. The invention in general comprises three electrodes adjustably spaced and adapted to have a large potential impressed between the outer electrodes. The central electrode includes two separate elements electrically connected togetaer and spaced apart to define a pair of spark gaps between the end electrodes. Means are provided to cause the gas flow in the switch to pass towards the central electrode, through a passage in each separate element, and out an exit disposed between the two separate central electrode elements in order to withdraw ions from the spark gap.

Hyperthyroidism hidden by congenital central hypoventilation syndrome.

PubMed

Fox, Danya A; Weese-Mayer, Debra E; Wensley, David F; Stewart, Laura L

2015-05-01

Congenital central hypoventilation syndrome (CCHS) is a rare neurocristopathy with severe central hypoventilation. CCHS results from a mutation in the paired-like homeobox 2B gene (PHOX2B). In addition to hypoventilation, patients with CCHS display a wide array of autonomic nervous system abnormalities, including decreased heart rate variability and abrupt sinus pauses, esophageal dysmotility, abnormal pupillary light response, and temperature dysregulation, to name a few. To date, there has been no documentation of a child with both CCHS and hyperthyroidism. We report the case of a young child with CCHS who presented with tachycardia, which was later found to be due to Grave's disease, after many months of investigation.

Is central dogma a global property of cellular information flow?

PubMed Central

Piras, Vincent; Tomita, Masaru; Selvarajoo, Kumar

2012-01-01

The central dogma of molecular biology has come under scrutiny in recent years. Here, we reviewed high-throughput mRNA and protein expression data of Escherichia coli, Saccharomyces cerevisiae, and several mammalian cells. At both single cell and population scales, the statistical comparisons between the entire transcriptomes and proteomes show clear correlation structures. In contrast, the pair-wise correlations of single transcripts to proteins show nullity. These data suggest that the organizing structure guiding cellular processes is observed at omics-wide scale, and not at single molecule level. The central dogma, thus, globally emerges as an average integrated flow of cellular information. PMID:23189060

Is central dogma a global property of cellular information flow?

PubMed

Piras, Vincent; Tomita, Masaru; Selvarajoo, Kumar

2012-01-01

The central dogma of molecular biology has come under scrutiny in recent years. Here, we reviewed high-throughput mRNA and protein expression data of Escherichia coli, Saccharomyces cerevisiae, and several mammalian cells. At both single cell and population scales, the statistical comparisons between the entire transcriptomes and proteomes show clear correlation structures. In contrast, the pair-wise correlations of single transcripts to proteins show nullity. These data suggest that the organizing structure guiding cellular processes is observed at omics-wide scale, and not at single molecule level. The central dogma, thus, globally emerges as an average integrated flow of cellular information.

Structure based alignment and clustering of proteins (STRALCP)

DOEpatents

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

2013-06-18

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

Transmission Reinforcements in the Central American Regional Power System

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

Elizondo, Marcelo A.; Vallem, Mallikarjuna R.; Samaan, Nader A.

The Central American regional interconnected power system (SER) connects the countries members of the Central American regional electricity market (MER): Guatemala, El Salvador, Honduras, Nicaragua, Costa Rica, and Panama. The SER was a result of a long term regional effort, and was initially conceived to transfer 300 MW between countries. However, the current transfer limits between countries range from 70 MW to 300 MW. Regional entities, like CRIE (Regional Commission of Electrical Interconnection), EOR (Central American Regional System Operator), and CDMER (Board of Directors of the Central American Market) are working on coordinating the national transmission expansion plans with regionalmore » transmission planning efforts. This paper presents experience in Central America region to recommend transmission reinforcements to achieve 300 MW transfer capacity between any pair of member countries of the Central American regional electricity market (MER). This paper also provides a methodology for technical analysis and for coordination among the regional and national entities. This methodology is unique for transmission systems of these characteristics.« less

Host–parasite behavioral interactions in a recently introduced, whooping crane population

USGS Publications Warehouse

King, Richard S.; McKann, Patrick C.; Gray, Brian R.; Putnam, Michael S.

2015-01-01

The whooping crane Grus americana has a long conservation history, but despite multiple attempts across North America, introduction success is lacking. Recently introduced, captively reared whooping cranes have had periods of poor reproductive performance in central Wisconsin that sometimes coincided with black fly (Diptera: Simuliidae) emergences. Sandhill crane Grus canadensis reproductive performance in central Wisconsin is approximately double that of whooping cranes. We used comfort behaviors as a measure of black fly harassment to infer whether behavioral differences existed between nesting sandhill cranes and nesting whooping cranes and between successful and unsuccessful whooping crane pairs. To further explore the interaction between black flies and incubating whooping cranes, we examined differences in behaviors between incubating birds and their off-nest mates. Compared to their off-nest mates, incubating whooping cranes exhibited elevated comfort behaviors, suggesting a bird at a nest may experience greater harassment from black flies. Sandhill cranes had elevated head-flicks over whooping cranes. Whooping cranes exhibited more head-rubs than sandhill cranes, and successful whooping crane pairs had elevated head-rubs over pairs that deserted their nests. Behavioral differences between sandhill cranes and whooping cranes as well as differences in reproductive performance, could be explained by exposure to local breeding conditions. Whereas sandhill cranes have nested in the area for hundreds, if not thousands, of years, whooping cranes were only recently introduced to the area. Behavioral differences between the species as well as those between successful and unsuccessful whooping crane pairs could also be explained by the effect of captive exposure, which could affect all whooping crane introductions.

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

PubMed Central

Villa, Alessandra

2017-01-01

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

Theoretical study on the binding mechanism between N6-methyladenine and natural DNA bases.

PubMed

Song, Qi-Xia; Ding, Zhen-Dong; Liu, Jian-Hua; Li, Yan; Wang, Hai-Jun

2013-03-01

N6-methyladenine (m(6)A) is a rare base naturally occurring in DNA. It is different from the base adenine due to its N-CH(3). Therefore, the base not only pairs with thymine, but also with other DNA bases (cytosine, adenine and guanine). In this work, Møller-Plesset second-order (MP2) method has been used to investigate the binding mechanism between m(6)A and natural DNA bases in gas phase and in aqueous solution. The results show that N-CH(3) changed the way of N6-methyladenine binding to natural DNA bases. The binding style significantly influences the stability of base pairs. The trans-m(6)A:G and trans-m(6)A:C conformers are the most stable among all the base pairs. The existence of solvent can remarkably reduce the stability of the base pairs, and the DNA bases prefer pairing with trans-m(6)A to cis-m(6)A. Besides, the properties of these hydrogen bonds have been analyzed by atom in molecules (AIM) theory, natural bond orbital (NBO) analysis and Wiberg bond indexes (WBI). In addition, pairing with m(6)A decreases the binding energies compared to the normal Watson-Crick base pairs, it may explain the instability of the N6 site methylated DNA in theory.

Validation of a Crowdsourcing Methodology for Developing a Knowledge Base of Related Problem-Medication Pairs.

PubMed

McCoy, A B; Wright, A; Krousel-Wood, M; Thomas, E J; McCoy, J A; Sittig, D F

2015-01-01

Clinical knowledge bases of problem-medication pairs are necessary for many informatics solutions that improve patient safety, such as clinical summarization. However, developing these knowledge bases can be challenging. We sought to validate a previously developed crowdsourcing approach for generating a knowledge base of problem-medication pairs in a large, non-university health care system with a widely used, commercially available electronic health record. We first retrieved medications and problems entered in the electronic health record by clinicians during routine care during a six month study period. Following the previously published approach, we calculated the link frequency and link ratio for each pair then identified a threshold cutoff for estimated problem-medication pair appropriateness through clinician review; problem-medication pairs meeting the threshold were included in the resulting knowledge base. We selected 50 medications and their gold standard indications to compare the resulting knowledge base to the pilot knowledge base developed previously and determine its recall and precision. The resulting knowledge base contained 26,912 pairs, had a recall of 62.3% and a precision of 87.5%, and outperformed the pilot knowledge base containing 11,167 pairs from the previous study, which had a recall of 46.9% and a precision of 83.3%. We validated the crowdsourcing approach for generating a knowledge base of problem-medication pairs in a large non-university health care system with a widely used, commercially available electronic health record, indicating that the approach may be generalizable across healthcare settings and clinical systems. Further research is necessary to better evaluate the knowledge, to compare crowdsourcing with other approaches, and to evaluate if incorporating the knowledge into electronic health records improves patient outcomes.

Validation of a Crowdsourcing Methodology for Developing a Knowledge Base of Related Problem-Medication Pairs

PubMed Central

Wright, A.; Krousel-Wood, M.; Thomas, E. J.; McCoy, J. A.; Sittig, D. F.

2015-01-01

Summary Background Clinical knowledge bases of problem-medication pairs are necessary for many informatics solutions that improve patient safety, such as clinical summarization. However, developing these knowledge bases can be challenging. Objective We sought to validate a previously developed crowdsourcing approach for generating a knowledge base of problem-medication pairs in a large, non-university health care system with a widely used, commercially available electronic health record. Methods We first retrieved medications and problems entered in the electronic health record by clinicians during routine care during a six month study period. Following the previously published approach, we calculated the link frequency and link ratio for each pair then identified a threshold cutoff for estimated problem-medication pair appropriateness through clinician review; problem-medication pairs meeting the threshold were included in the resulting knowledge base. We selected 50 medications and their gold standard indications to compare the resulting knowledge base to the pilot knowledge base developed previously and determine its recall and precision. Results The resulting knowledge base contained 26,912 pairs, had a recall of 62.3% and a precision of 87.5%, and outperformed the pilot knowledge base containing 11,167 pairs from the previous study, which had a recall of 46.9% and a precision of 83.3%. Conclusions We validated the crowdsourcing approach for generating a knowledge base of problem-medication pairs in a large non-university health care system with a widely used, commercially available electronic health record, indicating that the approach may be generalizable across healthcare settings and clinical systems. Further research is necessary to better evaluate the knowledge, to compare crowdsourcing with other approaches, and to evaluate if incorporating the knowledge into electronic health records improves patient outcomes. PMID:26171079

Using text analysis to quantify the similarity and evolution of scientific disciplines

PubMed Central

Dias, Laércio; Scharloth, Joachim

2018-01-01

We use an information-theoretic measure of linguistic similarity to investigate the organization and evolution of scientific fields. An analysis of almost 20 M papers from the past three decades reveals that the linguistic similarity is related but different from experts and citation-based classifications, leading to an improved view on the organization of science. A temporal analysis of the similarity of fields shows that some fields (e.g. computer science) are becoming increasingly central, but that on average the similarity between pairs of disciplines has not changed in the last decades. This suggests that tendencies of convergence (e.g. multi-disciplinarity) and divergence (e.g. specialization) of disciplines are in balance. PMID:29410857

Using text analysis to quantify the similarity and evolution of scientific disciplines.

PubMed

Dias, Laércio; Gerlach, Martin; Scharloth, Joachim; Altmann, Eduardo G

2018-01-01

We use an information-theoretic measure of linguistic similarity to investigate the organization and evolution of scientific fields. An analysis of almost 20 M papers from the past three decades reveals that the linguistic similarity is related but different from experts and citation-based classifications, leading to an improved view on the organization of science. A temporal analysis of the similarity of fields shows that some fields (e.g. computer science) are becoming increasingly central, but that on average the similarity between pairs of disciplines has not changed in the last decades. This suggests that tendencies of convergence (e.g. multi-disciplinarity) and divergence (e.g. specialization) of disciplines are in balance.

Chemistry, mechanism and clinical status of antisense oligonucleotides and duplex RNAs

PubMed Central

Shen, Xiulong; Corey, David R

2018-01-01

Abstract RNA plays a central role in the expression of all genes. Because any sequence within RNA can be recognized by complementary base pairing, synthetic oligonucleotides and oligonucleotide mimics offer a general strategy for controlling processes that affect disease. The two primary antisense approaches for regulating expression through recognition of cellular RNAs are single-stranded antisense oligonucleotides and duplex RNAs. This review will discuss the chemical modifications and molecular mechanisms that make synthetic nucleic acid drugs possible. Lessons learned from recent clinical trials will be summarized. Ongoing clinical trials are likely to decisively test the adequacy of our current generation of antisense nucleic acid technologies and highlight areas where more basic research is needed. PMID:29240946

Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide-protein complexes.

PubMed

Kondo, Jiro; Westhof, Eric

2011-10-01

Nucleotide bases are recognized by amino acid residues in a variety of DNA/RNA binding and nucleotide binding proteins. In this study, a total of 446 crystal structures of nucleotide-protein complexes are analyzed manually and pseudo pairs together with single and bifurcated hydrogen bonds observed between bases and amino acids are classified and annotated. Only 5 of the 20 usual amino acid residues, Asn, Gln, Asp, Glu and Arg, are able to orient in a coplanar fashion in order to form pseudo pairs with nucleotide bases through two hydrogen bonds. The peptide backbone can also form pseudo pairs with nucleotide bases and presents a strong bias for binding to the adenine base. The Watson-Crick side of the nucleotide bases is the major interaction edge participating in such pseudo pairs. Pseudo pairs between the Watson-Crick edge of guanine and Asp are frequently observed. The Hoogsteen edge of the purine bases is a good discriminatory element in recognition of nucleotide bases by protein side chains through the pseudo pairing: the Hoogsteen edge of adenine is recognized by various amino acids while the Hoogsteen edge of guanine is only recognized by Arg. The sugar edge is rarely recognized by either the side-chain or peptide backbone of amino acid residues.

Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide–protein complexes

PubMed Central

Kondo, Jiro; Westhof, Eric

2011-01-01

Nucleotide bases are recognized by amino acid residues in a variety of DNA/RNA binding and nucleotide binding proteins. In this study, a total of 446 crystal structures of nucleotide–protein complexes are analyzed manually and pseudo pairs together with single and bifurcated hydrogen bonds observed between bases and amino acids are classified and annotated. Only 5 of the 20 usual amino acid residues, Asn, Gln, Asp, Glu and Arg, are able to orient in a coplanar fashion in order to form pseudo pairs with nucleotide bases through two hydrogen bonds. The peptide backbone can also form pseudo pairs with nucleotide bases and presents a strong bias for binding to the adenine base. The Watson–Crick side of the nucleotide bases is the major interaction edge participating in such pseudo pairs. Pseudo pairs between the Watson–Crick edge of guanine and Asp are frequently observed. The Hoogsteen edge of the purine bases is a good discriminatory element in recognition of nucleotide bases by protein side chains through the pseudo pairing: the Hoogsteen edge of adenine is recognized by various amino acids while the Hoogsteen edge of guanine is only recognized by Arg. The sugar edge is rarely recognized by either the side-chain or peptide backbone of amino acid residues. PMID:21737431

Closing loop base pairs in RNA loop-loop complexes: structural behavior, interaction energy and solvation analysis through molecular dynamics simulations.

PubMed

Golebiowski, Jérôme; Antonczak, Serge; Fernandez-Carmona, Juan; Condom, Roger; Cabrol-Bass, Daniel

2004-12-01

Nanosecond molecular dynamics using the Ewald summation method have been performed to elucidate the structural and energetic role of the closing base pair in loop-loop RNA duplexes neutralized by Mg2+ counterions in aqueous phases. Mismatches GA, CU and Watson-Crick GC base pairs have been considered for closing the loop of an RNA in complementary interaction with HIV-1 TAR. The simulations reveal that the mismatch GA base, mediated by a water molecule, leads to a complex that presents the best compromise between flexibility and energetic contributions. The mismatch CU base pair, in spite of the presence of an inserted water molecule, is too short to achieve a tight interaction at the closing-loop junction and seems to force TAR to reorganize upon binding. An energetic analysis has allowed us to quantify the strength of the interactions of the closing and the loop-loop pairs throughout the simulations. Although the water-mediated GA closing base pair presents an interaction energy similar to that found on fully geometry-optimized structure, the water-mediated CU closing base pair energy interaction reaches less than half the optimal value.

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

PubMed

Brovarets', O O

2013-01-01

At the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of theory it was established for the first time, that the Löwdin's G*.C* DNA base pair formed by the mutagenic tautomers can acquire, as the A-T Watson-Crick DNA base pair, four biologically important configurations, namely: Watson-Crick, reverse Watson-Crick, Hoogsteen and reverse Hoogsteen. This fact demonstrates rather unexpected role of the tautomerisation of the one of the Watson-Crick DNA base pairs, in particular, via double proton transfer: exactly the G.C-->G*.C* tautomerisation allows to overcome steric hindrances for the implementation of the above mentioned configurations. Geometric, electron-topological and energetic properties of the H-bonds that stabilise the studied pairs, as well as the energetic characteristics of the latters are presented.

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

Leszczynski, Jerzy; Sponer, Judit; Sponer, Jiri

Recent experimental studies on the Watson Crick type base pairing of triazine and aminopyrimidine derivatives suggest that acid/base properties of the constituent bases might be related to the duplex stabilities measured in solution. Herein we use high-level quantum chemical calculations and molecular dynamics simulations to evaluate the base pairing and stacking interactions of seven selected base pairs, which are common in that they are stabilized by two NH O hydrogen bonds separated by one NH N hydrogen bond. We show that neither the base pairing nor the base stacking interaction energies correlate with the reported pKa data of the basesmore » and the melting points of the duplexes. This suggests that the experimentally observed correlation between the melting point data of the duplexes and the pKa values of the constituent bases is not rooted in the intrinsic base pairing and stacking properties. The physical chemistry origin of the observed experimental correlation thus remains unexplained and requires further investigations. In addition, since our calculations are carried out with extrapolation to the complete basis set of atomic orbitals and with inclusion of higher electron correlation effects, they provide reference data for stacking and base pairing energies of non-natural bases.« less

Thermal transport in topological-insulator-based superconducting hybrid structures with mixed singlet and triplet pairing states.

PubMed

Li, Hai; Zhao, Yuan Yuan

2017-11-22

In the framework of the Bogoliubov-de Gennes equation, we investigate the thermal transport properties in topological-insulator-based superconducting hybrid structures with mixed spin-singlet and spin-triplet pairing states, and emphasize the different manifestations of the spin-singlet and spin-triplet pairing states in the thermal transport signatures. It is revealed that the temperature-dependent differential thermal conductance strongly depends on the components of the pairing state, and the negative differential thermal conductance only occurs in the spin-singlet pairing state dominated regime. It is also found that the thermal conductance is profoundly sensitive to the components of the pairing state. In the spin-singlet pairing state controlled regime, the thermal conductance obviously oscillates with the phase difference and junction length. With increasing the proportion of the spin-triplet pairing state, the oscillating characteristic of the thermal conductance fades out distinctly. These results suggest an alternative route for distinguishing the components of pairing states in topological-insulator-based superconducting hybrid structures.

Top-pair production at the LHC through NNLO QCD and NLO EW

NASA Astrophysics Data System (ADS)

Czakon, Michał; Heymes, David; Mitov, Alexander; Pagani, Davide; Tsinikos, Ioannis; Zaro, Marco

2017-10-01

In this work we present for the first time predictions for top-quark pair differential distributions at the LHC at NNLO QCD accuracy and including EW corrections. For the latter we include not only contributions of O({α}_s^2α ) , but also those of order O({α}_s{α}^2) and O({α}^3) . Besides providing phenomenological predictions for all main differential distributions with stable top quarks, we also study the following issues. 1) The effect of the photon PDF on top-pair spectra: we find it to be strongly dependent on the PDF set used — especially for the top p T distribution. 2) The difference between the additive and multiplicative approaches for combining QCD and EW corrections: with our scale choice, we find relatively small differences between the central predictions, but reduced scale dependence within the multiplicative approach. 3) The potential effect from the radiation of heavy bosons on inclusive top-pair spectra: we find it to be, typically, negligible.

Divorce and infidelity are associated with skewed adult sex ratios in birds.

PubMed

Liker, András; Freckleton, Robert P; Székely, Tamás

2014-04-14

Adult sex ratio (ASR) is a fundamental concept in population demography, and recent theory suggests that ASR plays a central role in social behavior, mating systems, and parental care. Unbalanced ASRs are predicted to influence pair-bond and mating behavior, since the rarer sex in the population has more potential partners to mate with than the more common sex. Here we use phylogenetic comparative analyses to test whether ASR is related to three major aspects of mating behavior: divorce, social polygamy, and pair-bond infidelity. ASR is strongly correlated with long-term pair bonds, since the divorce rate is higher in species with a female-biased sex ratio, indicating that mate change by pair members and/or breaking of pair bonds by unmated individuals is more frequent when females outnumber males. Short-term pair bonds are also associated with unbalanced ASRs: males are more commonly polygamous when females outnumber males, and conversely, females are more polygamous when males outnumber females. Furthermore, infidelity increases with male-biased ASR in socially monogamous birds, suggesting that male coercion and/or female willingness to cheat the partner are facilitated by male-biased ASR. Our results provide the first comprehensive support for the proposition that ASR influences multiple aspects of pair-bond and mating behavior in wild populations. Copyright © 2014 Elsevier Ltd. All rights reserved.

Network-based analysis of differentially expressed genes in cerebrospinal fluid (CSF) and blood reveals new candidate genes for multiple sclerosis

PubMed Central

Safari-Alighiarloo, Nahid; Taghizadeh, Mohammad; Tabatabaei, Seyyed Mohammad; Namaki, Saeed

2016-01-01

Background The involvement of multiple genes and missing heritability, which are dominant in complex diseases such as multiple sclerosis (MS), entail using network biology to better elucidate their molecular basis and genetic factors. We therefore aimed to integrate interactome (protein–protein interaction (PPI)) and transcriptomes data to construct and analyze PPI networks for MS disease. Methods Gene expression profiles in paired cerebrospinal fluid (CSF) and peripheral blood mononuclear cells (PBMCs) samples from MS patients, sampled in relapse or remission and controls, were analyzed. Differentially expressed genes which determined only in CSF (MS vs. control) and PBMCs (relapse vs. remission) separately integrated with PPI data to construct the Query-Query PPI (QQPPI) networks. The networks were further analyzed to investigate more central genes, functional modules and complexes involved in MS progression. Results The networks were analyzed and high centrality genes were identified. Exploration of functional modules and complexes showed that the majority of high centrality genes incorporated in biological pathways driving MS pathogenesis. Proteasome and spliceosome were also noticeable in enriched pathways in PBMCs (relapse vs. remission) which were identified by both modularity and clique analyses. Finally, STK4, RB1, CDKN1A, CDK1, RAC1, EZH2, SDCBP genes in CSF (MS vs. control) and CDC37, MAP3K3, MYC genes in PBMCs (relapse vs. remission) were identified as potential candidate genes for MS, which were the more central genes involved in biological pathways. Discussion This study showed that network-based analysis could explicate the complex interplay between biological processes underlying MS. Furthermore, an experimental validation of candidate genes can lead to identification of potential therapeutic targets. PMID:28028462

Determinants of Chromosome Architecture: Insulator Pairing in cis and in trans

PubMed Central

Fujioka, Miki; Mistry, Hemlata; Schedl, Paul; Jaynes, James B.

2016-01-01

The chromosomes of multicellular animals are organized into a series of topologically independent looped domains. This domain organization is critical for the proper utilization and propagation of the genetic information encoded by the chromosome. A special set of architectural elements, called boundaries or insulators, are responsible both for subdividing the chromatin into discrete domains and for determining the topological organization of these domains. Central to the architectural functions of insulators are homologous and heterologous insulator:insulator pairing interactions. The former (pairing between copies of the same insulator) dictates the process of homolog alignment and pairing in trans, while the latter (pairing between different insulators) defines the topology of looped domains in cis. To elucidate the principles governing these architectural functions, we use two insulators, Homie and Nhomie, that flank the Drosophila even skipped locus. We show that homologous insulator interactions in trans, between Homie on one homolog and Homie on the other, or between Nhomie on one homolog and Nhomie on the other, mediate transvection. Critically, these homologous insulator:insulator interactions are orientation-dependent. Consistent with a role in the alignment and pairing of homologs, self-pairing in trans is head-to-head. Head-to-head self-interactions in cis have been reported for other fly insulators, suggesting that this is a general principle of self-pairing. Homie and Nhomie not only pair with themselves, but with each other. Heterologous Homie-Nhomie interactions occur in cis, and we show that they serve to delimit a looped chromosomal domain that contains the even skipped transcription unit and its associated enhancers. The topology of this loop is defined by the heterologous pairing properties of Homie and Nhomie. Instead of being head-to-head, which would generate a circular loop, Homie-Nhomie pairing is head-to-tail. Head-to-tail pairing in cis generates a stem-loop, a configuration much like that observed in classical lampbrush chromosomes. These pairing principles provide a mechanistic underpinning for the observed topologies within and between chromosomes. PMID:26910731

Genetic and DNA sequence analysis of the kanamycin resistance transposon Tn903.

PubMed Central

Grindley, N D; Joyce, C M

1980-01-01

The kanamycin resistance transposon Tn903 consists of a unique region of about 1000 base pairs bounded by a pair of 1050-base-pair inverted repeat sequences. Each repeat contains two Pvu II endonuclease cleavage sites separated by 520 base pairs. We have constructed derivatives of Tn903 in which this 520-base-pair fragment is deleted from one or both repeats. Those derivatives that lack both 520-base-pair fragments cannot transpose, whereas those that lack just one remain transposition proficient. One such transposable derivative, Tn903 delta I, has been selected for further study. We have determined the sequence of the intact inverted repeat. The 18 base pairs at each end are identical and inverted relative to one another, a structure characteristic of insertion sequences. Additional experiments indicate that a single inverted repeat from Tn903 can, in fact, transpose; we propose that this element be called IS903. To correlate the DNA sequence with genetic activities, we have created mutations by inserting a 10-base-pair DNA fragment at several sites within the intact repeat of Tn903 delta 1, and we have examined the effect of such insertions on transposability. The results suggest that IS903 encodes a 307-amino-acid polypeptide (a "transposase") that is absolutely required for transposition of IS903 or Tn903. Images PMID:6261245

Feedback-Driven Trial-by-Trial Learning in Autism Spectrum Disorders

PubMed Central

Solomon, Marjorie; Frank, Michael J.; Ragland, J. Daniel; Smith, Anne C.; Niendam, Tara A.; Lesh, Tyler A.; Grayson, David S.; Beck, Jonathan S.; Matter, John C.; Carter, Cameron S.

2017-01-01

Objective Impairments in learning are central to autism spectrum disorders. The authors investigated the cognitive and neural basis of these deficits in young adults with autism spectrum disorders using a well-characterized probabilistic reinforcement learning paradigm. Method The probabilistic selection task was implemented among matched participants with autism spectrum disorders (N=22) and with typical development (N=25), aged 18–40 years, using rapid event-related functional MRI. Participants were trained to choose the correct stimulus in high-probability (AB), medium-probability (CD), and low-probability (EF) pairs, presented with valid feedback 80%, 70%, and 60% of the time, respectively. Whole-brain voxel-wise and parametric modulator analyses examined early and late learning during the stimulus and feedback epochs of the task. Results The groups exhibited comparable performance on medium- and low-probability pairs. Typically developing persons showed higher accuracy on the high-probability pair, better win-stay performance (selection of the previously rewarded stimulus on the next trial of that type), and more robust recruitment of the anterior and medial prefrontal cortex during the stimulus epoch, suggesting development of an intact reward-based working memory for recent stimulus values. Throughout the feedback epoch, individuals with autism spectrum disorders exhibited greater recruitment of the anterior cingulate and orbito-frontal cortices compared with individuals with typical development, indicating continuing trial-by-trial activity related to feedback processing. Conclusions Individuals with autism spectrum disorders exhibit learning deficits reflecting impaired ability to develop an effective reward-based working memory to guide stimulus selection. Instead, they continue to rely on trial-by-trial feedback processing to support learning dependent upon engagement of the anterior cingulate and orbito-frontal cortices. PMID:25158242

GenoMycDB: a database for comparative analysis of mycobacterial genes and genomes.

PubMed

Catanho, Marcos; Mascarenhas, Daniel; Degrave, Wim; Miranda, Antonio Basílio de

2006-03-31

Several databases and computational tools have been created with the aim of organizing, integrating and analyzing the wealth of information generated by large-scale sequencing projects of mycobacterial genomes and those of other organisms. However, with very few exceptions, these databases and tools do not allow for massive and/or dynamic comparison of these data. GenoMycDB (http://www.dbbm.fiocruz.br/GenoMycDB) is a relational database built for large-scale comparative analyses of completely sequenced mycobacterial genomes, based on their predicted protein content. Its central structure is composed of the results obtained after pair-wise sequence alignments among all the predicted proteins coded by the genomes of six mycobacteria: Mycobacterium tuberculosis (strains H37Rv and CDC1551), M. bovis AF2122/97, M. avium subsp. paratuberculosis K10, M. leprae TN, and M. smegmatis MC2 155. The database stores the computed similarity parameters of every aligned pair, providing for each protein sequence the predicted subcellular localization, the assigned cluster of orthologous groups, the features of the corresponding gene, and links to several important databases. Tables containing pairs or groups of potential homologs between selected species/strains can be produced dynamically by user-defined criteria, based on one or multiple sequence similarity parameters. In addition, searches can be restricted according to the predicted subcellular localization of the protein, the DNA strand of the corresponding gene and/or the description of the protein. Massive data search and/or retrieval are available, and different ways of exporting the result are offered. GenoMycDB provides an on-line resource for the functional classification of mycobacterial proteins as well as for the analysis of genome structure, organization, and evolution.

Development and Validation of a Taiwanese Communication Progression in Science Education

ERIC Educational Resources Information Center

Hsin, Ming-Chin; Chien, Sung-pei; Hsu, Yin-Shao; Lin, Chen-Yung; Yore, Larry D.

2016-01-01

Common core standards, interdisciplinary education, and discipline-specific literacy are common international education reforms. The constructive-interpretative language arts pairs (speaking-listening, writing-reading, representing-viewing) and the communication, construction, and persuasion functions of language are central in these movements.…

Dandy-Walker malformation with postaxial polydactly: a new case of Pierquin syndrome.

PubMed

Passalacqua, Cristóbal A; Villegas, Victor P; Aracena, Mariana I; Mellado, Cecilia X

2013-04-01

The combination of Dandy-Walker malformation, other central nervous system anomalies, and postaxial polydactyly has been reported previously in two pairs of siblings. We propose the name 'Pierquin syndrome' for this combination and we report a new patient with this disorder.

47 CFR 22.719 - Additional channel policy for rural radiotelephone stations.

Code of Federal Regulations, 2012 CFR

2012-10-01

... radiotelephone stations. 22.719 Section 22.719 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED... policy for rural radiotelephone stations. The rules in this section govern the processing of applications for central office stations that request a rural radiotelephone channel pair when the applicant has...

Energy dependence of Kπ, pπ and Kp fluctuations in Au+Au collisions from √s NN=7.7 to 200 GeV

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

Adamczyk, L.

A search for the quantum chromodynamics (QCD) critical point was performed by the STAR experiment at the Relativistic Heavy Ion Collider, using dynamical fluctuations of unlike particle pairs. Heavy ion collisions were studied over a large range of collision energies with homogeneous acceptance and excellent particle identification, covering a significant range in the QCD phase diagram where a critical point may be located. Dynamical Kπ, pπ, and Kp fluctuations as measured by the STAR experiment in central 0–5% Au+Au collisions from center-of-mass collision energies √s NN=7.7 to 200 GeV are presented. The observable νdyn was used to quantify the magnitudemore » of the dynamical fluctuations in event-by-event measurements of the Kπ, pπ, and Kp pairs. The energy dependences of these fluctuations from central 0–5% Au+Au collisions all demonstrate a smooth evolution with collision energy.« less

In situ fossil seedlings of a Metasequoia-like taxodiaceous conifer from Paleocene river floodplain deposits of central Alberta, Canada.

PubMed

Falder, A B; Stockey, R A; Rothwell, G W

1999-06-01

Fossil seeds and seedlings of a Metasequoia-like taxodiaceous conifer occur in Paleocene deposits at the Munce's Hill and Gao Mine localities of central Alberta, Canada. Compression/impression specimens are preserved in upright growth positions among seedlings of the cercidiphyllaceous dicot Joffrea speirsii Crane & Stockey. There are a large number of seeds, a few of which were buried while germinating and show a radicle or short primary root. More than 500 Metasequoia-like seedlings have been identified that have two linear cotyledons with parallel margins and rounded tips. Three specimens have been found that display three cotyledons. Slightly older seedlings show decussate pairs of leaves attached to the stem distal to the cotyledons. Still older seedlings have axillary branches that show varying sizes and numbers of opposite leaves arranged in a single plane distal to the opposite pairs. These specimens reveal that both Joffrea and this extinct taxodiaceous conifer were early colonizers of North American floodplain communities at the beginning of the Tertiary.

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

PubMed

Tateishi-Karimata, Hisae; Nakano, Miki; Sugimoto, Naoki

2014-01-08

The instability of Hoogsteen base pairs relative to Watson-Crick base pairs has limited biological applications of triplex-forming oligonucleotides. Hydrated ionic liquids (ILs) provide favourable environments for a wide range of chemical reactions and are known to impact the stabilities of Watson-Crick base pairs. We found that DNA triplex formation was significantly stabilized in hydrated choline dihydrogen phosphate as compared with an aqueous buffer at neutral pH. Interestingly, the stability of Hoogsteen base pairs was found to be comparable with that of Watson-Crick base pairs in the hydrated IL. Molecular dynamics simulations of a DNA triplex in the presence of choline ions revealed that the DNA triplex was stabilized because of the binding of choline ion around the third strand in the grooves. Our finding will facilitate the development of new DNA materials. Our data also indicate that triplex formation may be stabilized inside cells where choline ions and their derivatives are abundant in vivo.

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

PubMed Central

Tateishi-Karimata, Hisae; Nakano, Miki; Sugimoto, Naoki

2014-01-01

The instability of Hoogsteen base pairs relative to Watson–Crick base pairs has limited biological applications of triplex-forming oligonucleotides. Hydrated ionic liquids (ILs) provide favourable environments for a wide range of chemical reactions and are known to impact the stabilities of Watson–Crick base pairs. We found that DNA triplex formation was significantly stabilized in hydrated choline dihydrogen phosphate as compared with an aqueous buffer at neutral pH. Interestingly, the stability of Hoogsteen base pairs was found to be comparable with that of Watson–Crick base pairs in the hydrated IL. Molecular dynamics simulations of a DNA triplex in the presence of choline ions revealed that the DNA triplex was stabilized because of the binding of choline ion around the third strand in the grooves. Our finding will facilitate the development of new DNA materials. Our data also indicate that triplex formation may be stabilized inside cells where choline ions and their derivatives are abundant in vivo. PMID:24399194

m1A and m1G Potently Disrupt A-RNA Structure Due to the Intrinsic Instability of Hoogsteen Base Pairs

PubMed Central

Zhou, Huiqing; Kimsey, Isaac J.; Nikolova, Evgenia N.; Sathyamoorthy, Bharathwaj; Grazioli, Gianmarc; McSally, James; Bai, Tianyu; Wunderlich, Christoph H.; Kreutz, Christoph; Andricioaei, Ioan; Al-Hashimi, Hashim M.

2016-01-01

The B-DNA double helix can dynamically accommodate G–C and A–T base pairs in either Watson-Crick or Hoogsteen configurations. Here, we show that G–C+ and A–U Hoogsteen base pairs are strongly disfavored in A-RNA. As a result, N1-methyl adenosine and N1-methyl guanosine, which occur in DNA as a form of alkylation damage, and in RNA as a posttranscriptional modification, have dramatically different consequences. They create G–C+ and A–U Hoogsteen base pairs in duplex DNA that maintain the structural integrity of the double helix, but block base pairing all together and induce local duplex melting in RNA, providing a mechanism for potently disrupting RNA structure through posttranscriptional modifications. The markedly different propensities to form Hoogsteen base pairs in B-DNA and A-RNA may help meet the opposing requirements of maintaining genome stability on one hand, and dynamically modulating the structure of the epitranscriptome on the other. PMID:27478929

Physiotherapy students and clinical educators perceive several ways in which incorporating peer-assisted learning could improve clinical placements: a qualitative study.

PubMed

Sevenhuysen, Samantha; Farlie, Melanie K; Keating, Jennifer L; Haines, Terry P; Molloy, Elizabeth

2015-04-01

What are the experiences of students and clinical educators in a paired student placement model incorporating facilitated peer-assisted learning (PAL) activities, compared to a traditional paired teaching approach? Qualitative study utilising focus groups. Twenty-four physiotherapy students and 12 clinical educators. Participants in this study had experienced two models of physiotherapy clinical undergraduate education: a traditional paired model (usual clinical supervision and learning activities led by clinical educators supervising pairs of students) and a PAL model (a standardised series of learning activities undertaken by student pairs and clinical educators to facilitate peer interaction using guided strategies). Peer-assisted learning appears to reduce the students' anxiety, enhance their sense of safety in the learning environment, reduce educator burden, maximise the use of downtime, and build professional skills including collaboration and feedback. While PAL adds to the clinical learning experience, it is not considered to be a substitute for observation of the clinical educator, expert feedback and guidance, or hands-on immersive learning activities. Cohesion of the student-student relationship was seen as an enabler of successful PAL. Students and educators perceive that PAL can help to position students as active learners through reduced dependence on the clinical educator, heightened roles in observing practice, and making and communicating evaluative judgments about quality of practice. The role of the clinical educator is not diminished with PAL, but rather is central in designing flexible and meaningful peer-based experiences and in balancing PAL with independent learning opportunities. ACTRN12610000859088. [Sevenhuysen S, Farlie MK, Keating JL, Haines TP, Molloy E (2015) Physiotherapy students and clinical educators perceive several ways in which incorporating peer-assisted learning could improve clinical placements: a qualitative study.Journal of Physiotherapy61: 87-92]. Crown Copyright © 2015. Published by Elsevier B.V. All rights reserved.

Fovea sparing internal limiting membrane peeling using multiple parafoveal curvilinear peels for myopic foveoschisis: technique and outcome.

PubMed

Jin, Haiying; Zhang, Qi; Zhao, Peiquan

2016-10-18

To introduce a modified surgical technique, the "parafoveal multiple curvelinear internal limiting membrane (ILM) peeling", to preserve epi-foveal ILM in myopic foveoschisis surgery. Consecutive patients with myopic foveoschisis were enrolled in the present prospective interventional case series. The surgeries were performed using transconjunctival 23-gauge system. The macular area was divided into quadrants. ILM was peeled off in a curvilinear manner centered around the site that was away from the central fovea in each quadrant. Shearing forces were used to control the direction to keep the peeling away from central fovea. ILM at central fovea of about 500 to 1000 μm was preserved by this technique. This technique was performed in 20 eyes of 20 consecutive patients. Epi-foveal ILM was successfully preserved in all cases using the technique. Patients were followed up for more than 12 months. The mean postoperative logMAR visual acuity improved from 1.67 ± 0.65 preoperatively to 1.15 ± 0.49 (P = 0.015; paired t-test). Postoperative OCT examinations showed that full-thickness macular holes (MHs) did not developed in any case. Central fovea thickness decreased from 910 ± 261 μm preoperatively to 125 ± 85 postoperatively (P = 0.001; paired t-test). Fovea sparing ILM peeling using multiple parafoveal curvilinear peels prevents the development of postoperative full-thickness MHs in eyes with myopic foveoschisis.

[Spatial organization of bioelectrical brain activity in epilepsy and amenorrhea of central genesis].

PubMed

Avakian, G N; Oleĭnikova, O M; Nerobkova, L N; Dovletkhanova, E R; Mitrofanov, A A; Gusev, E I

2002-01-01

The study aimed at modification of co-herent analysis (CA), as a mathematical method for EEG data processing for objective evaluation of bioelectric brain activity spatial organization in women with epilepsy and secondary amenorrhea of central genesis. One hundred sixty one women (30 with epilepsy, 116 with amenorrhea and 115 controls aged 15 to 41 years) have been examined. Characteristic changes of cortico-cortical inter- and intra-hemisphere relations for patients with catamenial (CTM) and noncatamenial (NCTM) epilepsy in different menstrual cycle terms were found. The most distinct changes were detected in theta-activity analysis. In the beginning of menstrual cycle, the patients with CTM epilepsy exhibited higher CA indices in theta-rhythm range in all right hemisphere pairs studied. On the contrary, patients with NCTM epilepsy exhibited lower CA indices mainly in the right brain hemisphere. alpha-rhythm spatial organization analysis in the same patients showed similar correlations, but they were better expressed in alpha-rhythm generation zone: in the beginning of menstrual cycle CA indices were high in patients with CTM epilepsy and low in those with NCTM epilepsy. Comparing to controls, patients with secondary amenorrhea of central genesis showed most distinct changes in theta-activity towards the CA indices increase in the majority of the leads. In patients with epilepsy and amenorrhea, CA indices of right brain hemisphere and intra-central temporal lead pairs were lower than in patients with amenorrhea without epilepsy by both alpha- and theta-rhythms.

Evidence for Strange Stellar Family (Artist Concept)

NASA Technical Reports Server (NTRS)

2007-01-01

This artist concept depicts a quadruple-star system called HD 98800. The system is approximately 10 million years old, and is located 150 light-years away in the constellation TW Hydrae.

HD 98800 contains four stars, which are paired off into doublets, or binaries. The stars in the binary pairs orbit around each other, and the two pairs also circle each other like choreographed ballerinas. One of the stellar pairs, called HD 98800B, has a disk of dust around it, while the other pair does not.

Although the four stars are gravitationally bound, the distance separating the two binary pairs is about 50 astronomical units (AU) -- slightly more than the average distance between our sun and Pluto.

Using NASA's Spitzer Space Telescope, scientists finally have a detailed view of HD 98800B's potential planet-forming disk. Astronomers used the telescope's infrared spectrometer to detect the presence of two belts in the disk made of large dust grains. One belt sits approximately 5.9 AU away from the central binary, or about the distance from the sun to Jupiter, and is likely made up of asteroids and comets. The other belt sits at 1.5 to 2 AU, comparable to the area where Mars and the asteroid belt sit, and is made up of sand-sized dust grains.

Conformation of the Phosphate D-alanine Zwitterion in Bacterial Teichoic Acid from Nuclear Magnetic Resonance Spectroscopy

PubMed Central

Garimella, Ravindranath; Halye, Jeffrey L.; Harrison, William; Klebba, Phillip E.; Rice, Charles V.

2009-01-01

The conformation of D-alanine (D-Ala) groups of bacterial teichoic acid is a central, yet untested, paradigm of microbiology. The D-Ala binds via the C-terminus, thereby allowing the amine to exist as a free cationic NH3+ group with the ability to form a contact-ion-pair with the nearby anionic phosphate group. This conformation hinders metal chelation by the phosphate because the zwitterion pair is charge neutral. To the contrary, the repulsion of cationic antimicrobial peptides (CAMPs) is attributed to the presence of the D-Ala cation; thus the ion-pair does not form in this model. Solid-state nuclear magnetic resonance (NMR) spectroscopy has been used to measure the distance between amine and phosphate groups within cell wall fragments of Bacillus subtilis. The bacteria were grown on media containing 15N D-Ala and β-chloroalanine racemase inhibitor. The rotational-echo double-resonance (REDOR) pulse sequence was used to measure the internuclear dipolar coupling and the results demonstrate: 1) the metal-free amine-to-phosphate distance is 4.4 Å and 2) the amine-to-phosphate distance increases to 5.4 Å in the presence of Mg2+ ions. As a result, the zwitterion exists in a nitrogen-oxygen ion-pair configuration providing teichoic acid with a positive charge to repel CAMPs. Additionally, the amine of D-Ala does not prevent magnesium chelation in contradiction to the prevailing view of teichoic acids in metal binding. Thus, the NMR-based description of teichoic acid structure resolves the contradictory models, advances the basic understanding of cell wall biochemistry, and provides possible insight into the creation of new antibiotic therapies. PMID:19746945

Development of a suspension microarray for the genotyping of African swine fever virus targeting the SNPs in the C-terminal end of the p72 gene region of the genome.

PubMed

Leblanc, N; Cortey, M; Fernandez Pinero, J; Gallardo, C; Masembe, C; Okurut, A R; Heath, L; van Heerden, J; Sánchez-Vizcaino, J M; Ståhl, K; Belák, S

2013-08-01

African swine fever virus (ASFV) causes one of the most dreaded transboundary animal diseases (TADs) in Suidae. African swine fever (ASF) often causes high rates of morbidity and mortality, which can reach 100% in domestic swine. To date, serological diagnosis has the drawback of not being able to differentiate variants of this virus. Previous studies have identified the 22 genotypes based on sequence variation in the C-terminal region of the p72 gene, which has become the standard for categorizing ASFVs. This article describes a genotyping assay developed using a segment of PCR-amplified genomic DNA of approximately 450 bp, which encompasses the C-terminal end of the p72 gene. Complementary paired DNA probes of 15 or 17 bp in length, which are identical except for a single nucleotide polymorphism (SNP) in the central position, were designed to either individually or in combination differentiate between the 22 genotypes. The assay was developed using xMAP technology; probes were covalently linked to microspheres, hybridized to PCR product, labelled with a reporter and read in the Luminex 200 analyzer. Characterization of the sample was performed by comparing fluorescence of the paired SNP probes, that is, the probe with higher fluorescence in a complementary pair identified the SNP that a particular sample possessed. In the final assay, a total of 52 probes were employed, 24 SNP pairs and 4 for general detection. One or more samples from each of the 22 genotypes were tested. The assay was able to detect and distinguish all 22 genotypes. This novel assay provides a powerful novel tool for the simultaneous rapid diagnosis and genotypic differentiation of ASF. © 2012 Blackwell Verlag GmbH.

Imidazopyridine/Pyrrole and hydroxybenzimidazole/pyrrole pairs for DNA minor groove recognition.

PubMed

Renneberg, Dorte; Dervan, Peter B

2003-05-14

The DNA binding properties of fused heterocycles imidazo[4,5-b]pyridine (Ip) and hydroxybenzimidazole (Hz) paired with pyrrole (Py) in eight-ring hairpin polyamides are reported. The recognition profile of Ip/Py and Hz/Py pairs were compared to the five-membered ring pairs Im/Py and Hp/Py on a DNA restriction fragment at four 6-base pair recognition sites which vary at a single position 5'-TGTNTA-3', where N = G, C, T, A. The Ip/Py pair distinguishes G.C from C.G, T.A, and A.T, and the Hz/Py pair distinguishes T.A from A.T, G.C, and C.G, affording a new set of heterocycle pairs to target the four Watson-Crick base pairs in the minor groove of DNA.

A Role for Central Nervous Growth Hormone-Releasing Hormone Signaling in the Consolidation of Declarative Memories

PubMed Central

Michel, Christian; Perras, Boris; Born, Jan

2011-01-01

Contributions of somatotropic hormonal activity to memory functions in humans, which are suggested by clinical observations, have not been systematically examined. With previous experiments precluding a direct effect of systemic growth hormone (GH) on acute memory formation, we assessed the role of central nervous somatotropic signaling in declarative memory consolidation. We examined the effect of intranasally administered growth hormone releasing-hormone (GHRH; 600 µg) that has direct access to the brain and suppresses endogenous GHRH via an ultra-short negative feedback loop. Twelve healthy young men learned word-pair associates at 2030 h and were administered GHRH and placebo, respectively, at 2100 h. Retrieval was tested after 11 hours of wakefulness. Compared to placebo, intranasal GHRH blunted GH release within 3 hours after substance administration and reduced the number of correctly recalled word-pairs by ∼12% (both P<0.05). The impairment of declarative memory consolidation was directly correlated to diminished GH concentrations (P<0.05). Procedural memory consolidation as examined by the parallel assessment of finger sequence tapping performance was not affected by GHRH administration. Our findings indicate that intranasal GHRH, by counteracting endogenous GHRH release, impairs hippocampal memory processing. They provide first evidence for a critical contribution of central nervous somatotropic activity to hippocampus-dependent memory consolidation. PMID:21850272

Stacking interactions and DNA intercalation

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

Li, Dr. Shen; Cooper, Valentino R; Thonhauser, Prof. Timo

2009-01-01

The relationship between stacking interactions and the intercalation of proflavine and ellipticine within DNA is investigated using a nonempirical van der Waals density functional for the correlation energy. Our results, employing a binary stack model, highlight fundamental, qualitative differences between base-pair base-pair interactions and that of the stacked intercalator base pair system. Most notable result is the paucity of torque which so distinctively defines the Twist of DNA. Surprisingly, this model, when combined with a constraint on the twist of the surrounding base-pair steps to match the observed unwinding of the sugar-phosphate backbone, was sufficient for explaining the experimentally observedmore » proflavine intercalator configuration. Our extensive mapping of the potential energy surface of base-pair intercalator interactions can provide valuable information for future nonempirical studies of DNA intercalation dynamics.« less

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

NASA Astrophysics Data System (ADS)

Guo, H.; Zhang, H.

2016-12-01

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

Transverse momentum dependence of D-meson production in Pb-Pb collisions at $$ \\sqrt{{\\mathrm{s}}_{\\mathrm{NN}}}=2.76 $$ TeV

DOE PAGES

Adam, J.; Adamová, D.; Aggarwal, M. M.; ...

2016-03-14

The production of prompt charmed mesons D 0, D + and D* +, and their antiparticles, was measured with the ALICE detector in Pb-Pb collisions at the centre-of-mass energy per nucleon pair, √ sNN, of 2.76 TeV. The production yields for rapidity |y| < 0.5 are presented as a function of transverse momentum, p T, in the interval 1–36 GeV/c for the centrality class 0–10% and in the interval 1–16 GeV/c for the centrality class 30–50%. The nuclear modification factor R AA was computed using a proton-proton reference at √s = 2.76 TeV, based on measurements at √s = 7more » TeV and on theoretical calculations. A maximum suppression by a factor of 5-6 with respect to binary-scaled pp yields is observed for the most central collisions at p T of about 10 GeV/c. A suppression by a factor of about 2-3 persists at the highest p T covered by the measurements. At low pT (1-3 GeV/c), the R AA has large uncertainties that span the range 0.35 (factor of about 3 suppression) to 1 (no suppression). In all p T intervals, the R AA is larger in the 30-50% centrality class compared to central collisions. Furthermore, the D-meson R AA is also compared with that of charged pions and, at large p T, charged hadrons, and with model calculations.« less

Transverse momentum dependence of D-meson production in Pb-Pb collisions at sqrt{{s}_{NN}}=2.76 TeV

NASA Astrophysics Data System (ADS)

Adam, J.; Adamová, D.; Aggarwal, M. M.; Aglieri Rinella, G.; Agnello, M.; Agrawal, N.; Ahammed, Z.; Ahn, S. U.; Aiola, S.; Akindinov, A.; Alam, S. N.; Aleksandrov, D.; Alessandro, B.; Alexandre, D.; Alfaro Molina, R.; Alici, A.; Alkin, A.; Almaraz, J. R. M.; Alme, J.; Alt, T.; Altinpinar, S.; Altsybeev, I.; Alves Garcia Prado, C.; Andrei, C.; Andronic, A.; Anguelov, V.; Anielski, J.; Antičić, T.; Antinori, F.; Antonioli, P.; Aphecetche, L.; Appelshäuser, H.; Arcelli, S.; Arnaldi, R.; Arnold, O. W.; Arsene, I. C.; Arslandok, M.; Audurier, B.; Augustinus, A.; Averbeck, R.; Azmi, M. D.; Badalà, A.; Baek, Y. W.; Bagnasco, S.; Bailhache, R.; Bala, R.; Baldisseri, A.; Baral, R. C.; Barbano, A. M.; Barbera, R.; Barile, F.; Barnaföldi, G. G.; Barnby, L. S.; Barret, V.; Bartalini, P.; Barth, K.; Bartke, J.; Bartsch, E.; Basile, M.; Bastid, N.; Basu, S.; Bathen, B.; Batigne, G.; Batista Camejo, A.; Batyunya, B.; Batzing, P. C.; Bearden, I. G.; Beck, H.; Bedda, C.; Behera, N. K.; Belikov, I.; Bellini, F.; Bello Martinez, H.; Bellwied, R.; Belmont, R.; Belmont-Moreno, E.; Belyaev, V.; Bencedi, G.; Beole, S.; Berceanu, I.; Bercuci, A.; Berdnikov, Y.; Berenyi, D.; Bertens, R. A.; Berzano, D.; Betev, L.; Bhasin, A.; Bhat, I. R.; Bhati, A. K.; Bhattacharjee, B.; Bhom, J.; Bianchi, L.; Bianchi, N.; Bianchin, C.; Bielčík, J.; Bielčíková, J.; Bilandzic, A.; Biswas, R.; Biswas, S.; Bjelogrlic, S.; Blair, J. T.; Blau, D.; Blume, C.; Bock, F.; Bogdanov, A.; Bøggild, H.; Boldizsár, L.; Bombara, M.; Book, J.; Borel, H.; Borissov, A.; Borri, M.; Bossú, F.; Botta, E.; Böttger, S.; Bourjau, C.; Braun-Munzinger, P.; Bregant, M.; Breitner, T.; Broker, T. A.; Browning, T. A.; Broz, M.; Brucken, E. J.; Bruna, E.; Bruno, G. E.; Budnikov, D.; Buesching, H.; Bufalino, S.; Buncic, P.; Busch, O.; Buthelezi, Z.; Butt, J. B.; Buxton, J. T.; Caffarri, D.; Cai, X.; Caines, H.; Calero Diaz, L.; Caliva, A.; Calvo Villar, E.; Camerini, P.; Carena, F.; Carena, W.; Carnesecchi, F.; Castillo Castellanos, J.; Castro, A. J.; Casula, E. A. R.; Ceballos Sanchez, C.; Cepila, J.; Cerello, P.; Cerkala, J.; Chang, B.; Chapeland, S.; Chartier, M.; Charvet, J. L.; Chattopadhyay, S.; Chattopadhyay, S.; Chelnokov, V.; Cherney, M.; Cheshkov, C.; Cheynis, B.; Chibante Barroso, V.; Chinellato, D. D.; Cho, S.; Chochula, P.; Choi, K.; Chojnacki, M.; Choudhury, S.; Christakoglou, P.; Christensen, C. H.; Christiansen, P.; Chujo, T.; Chung, S. U.; Cicalo, C.; Cifarelli, L.; Cindolo, F.; Cleymans, J.; Colamaria, F.; Colella, D.; Collu, A.; Colocci, M.; Conesa Balbastre, G.; Conesa del Valle, Z.; Connors, M. E.; Contreras, J. G.; Cormier, T. M.; Corrales Morales, Y.; Cortés Maldonado, I.; Cortese, P.; Cosentino, M. R.; Costa, F.; Crochet, P.; Cruz Albino, R.; Cuautle, E.; Cunqueiro, L.; Dahms, T.; Dainese, A.; Danu, A.; Das, D.; Das, I.; Das, S.; Dash, A.; Dash, S.; De, S.; De Caro, A.; de Cataldo, G.; de Conti, C.; de Cuveland, J.; De Falco, A.; De Gruttola, D.; De Marco, N.; De Pasquale, S.; Deisting, A.; Deloff, A.; Dénes, E.; Deplano, C.; Dhankher, P.; Di Bari, D.; Di Mauro, A.; Di Nezza, P.; Diaz Corchero, M. A.; Dietel, T.; Dillenseger, P.; Divià, R.; Djuvsland, Ø.; Dobrin, A.; Domenicis Gimenez, D.; Dönigus, B.; Dordic, O.; Drozhzhova, T.; Dubey, A. K.; Dubla, A.; Ducroux, L.; Dupieux, P.; Ehlers, R. J.; Elia, D.; Engel, H.; Epple, E.; Erazmus, B.; Erdemir, I.; Erhardt, F.; Espagnon, B.; Estienne, M.; Esumi, S.; Eum, J.; Evans, D.; Evdokimov, S.; Eyyubova, G.; Fabbietti, L.; Fabris, D.; Faivre, J.; Fantoni, A.; Fasel, M.; Feldkamp, L.; Feliciello, A.; Feofilov, G.; Ferencei, J.; Fernández Téllez, A.; Ferreiro, E. G.; Ferretti, A.; Festanti, A.; Feuillard, V. J. G.; Figiel, J.; Figueredo, M. A. S.; Filchagin, S.; Finogeev, D.; Fionda, F. M.; Fiore, E. M.; Fleck, M. G.; Floris, M.; Foertsch, S.; Foka, P.; Fokin, S.; Fragiacomo, E.; Francescon, A.; Frankenfeld, U.; Fuchs, U.; Furget, C.; Furs, A.; Fusco Girard, M.; Gaardhøje, J. J.; Gagliardi, M.; Gago, A. M.; Gallio, M.; Gangadharan, D. R.; Ganoti, P.; Gao, C.; Garabatos, C.; Garcia-Solis, E.; Gargiulo, C.; Gasik, P.; Gauger, E. F.; Germain, M.; Gheata, A.; Gheata, M.; Ghosh, P.; Ghosh, S. K.; Gianotti, P.; Giubellino, P.; Giubilato, P.; Gladysz-Dziadus, E.; Glässel, P.; Goméz Coral, D. M.; Gomez Ramirez, A.; Gonzalez, V.; González-Zamora, P.; Gorbunov, S.; Görlich, L.; Gotovac, S.; Grabski, V.; Grachov, O. A.; Graczykowski, L. K.; Graham, K. L.; Grelli, A.; Grigoras, A.; Grigoras, C.; Grigoriev, V.; Grigoryan, A.; Grigoryan, S.; Grinyov, B.; Grion, N.; Gronefeld, J. M.; Grosse-Oetringhaus, J. F.; Grossiord, J.-Y.; Grosso, R.; Guber, F.; Guernane, R.; Guerzoni, B.; Gulbrandsen, K.; Gunji, T.; Gupta, A.; Gupta, R.; Haake, R.; Haaland, Ø.; Hadjidakis, C.; Haiduc, M.; Hamagaki, H.; Hamar, G.; Harris, J. W.; Harton, A.; Hatzifotiadou, D.; Hayashi, S.; Heckel, S. T.; Heide, M.; Helstrup, H.; Herghelegiu, A.; Herrera Corral, G.; Hess, B. A.; Hetland, K. F.; Hillemanns, H.; Hippolyte, B.; Hosokawa, R.; Hristov, P.; Huang, M.; Humanic, T. J.; Hussain, N.; Hussain, T.; Hutter, D.; Hwang, D. S.; Ilkaev, R.; Inaba, M.; Ippolitov, M.; Irfan, M.; Ivanov, M.; Ivanov, V.; Izucheev, V.; Jacobs, P. M.; Jadhav, M. B.; Jadlovska, S.; Jadlovsky, J.; Jahnke, C.; Jakubowska, M. J.; Jang, H. J.; Janik, M. A.; Jayarathna, P. H. S. Y.; Jena, C.; Jena, S.; Jimenez Bustamante, R. T.; Jones, P. G.; Jung, H.; Jusko, A.; Kalinak, P.; Kalweit, A.; Kamin, J.; Kang, J. H.; Kaplin, V.; Kar, S.; Karasu Uysal, A.; Karavichev, O.; Karavicheva, T.; Karayan, L.; Karpechev, E.; Kebschull, U.; Keidel, R.; Keijdener, D. L. D.; Keil, M.; Mohisin Khan, M.; Khan, P.; Khan, S. A.; Khanzadeev, A.; Kharlov, Y.; Kileng, B.; Kim, D. W.; Kim, D. J.; Kim, D.; Kim, H.; Kim, J. S.; Kim, M.; Kim, M.; Kim, S.; Kim, T.; Kirsch, S.; Kisel, I.; Kiselev, S.; Kisiel, A.; Kiss, G.; Klay, J. L.; Klein, C.; Klein, J.; Klein-Bösing, C.; Klewin, S.; Kluge, A.; Knichel, M. L.; Knospe, A. G.; Kobayashi, T.; Kobdaj, C.; Kofarago, M.; Kollegger, T.; Kolojvari, A.; Kondratiev, V.; Kondratyeva, N.; Kondratyuk, E.; Konevskikh, A.; Kopcik, M.; Kour, M.; Kouzinopoulos, C.; Kovalenko, O.; Kovalenko, V.; Kowalski, M.; Koyithatta Meethaleveedu, G.; Králik, I.; Kravčáková, A.; Kretz, M.; Krivda, M.; Krizek, F.; Kryshen, E.; Krzewicki, M.; Kubera, A. M.; Kučera, V.; Kuhn, C.; Kuijer, P. G.; Kumar, A.; Kumar, J.; Kumar, L.; Kumar, S.; Kurashvili, P.; Kurepin, A.; Kurepin, A. B.; Kuryakin, A.; Kweon, M. J.; Kwon, Y.; La Pointe, S. L.; La Rocca, P.; Ladron de Guevara, P.; Lagana Fernandes, C.; Lakomov, I.; Langoy, R.; Lara, C.; Lardeux, A.; Lattuca, A.; Laudi, E.; Lea, R.; Leardini, L.; Lee, G. R.; Lee, S.; Lehas, F.; Lemmon, R. C.; Lenti, V.; Leogrande, E.; León Monzón, I.; León Vargas, H.; Leoncino, M.; Lévai, P.; Li, S.; Li, X.; Lien, J.; Lietava, R.; Lindal, S.; Lindenstruth, V.; Lippmann, C.; Lisa, M. A.; Ljunggren, H. M.; Lodato, D. F.; Loenne, P. I.; Loginov, V.; Loizides, C.; Lopez, X.; López Torres, E.; Lowe, A.; Luettig, P.; Lunardon, M.; Luparello, G.; Maevskaya, A.; Mager, M.; Mahajan, S.; Mahmood, S. M.; Maire, A.; Majka, R. D.; Malaev, M.; Maldonado Cervantes, I.; Malinina, L.; Mal'Kevich, D.; Malzacher, P.; Mamonov, A.; Manko, V.; Manso, F.; Manzari, V.; Marchisone, M.; Mareš, J.; Margagliotti, G. V.; Margotti, A.; Margutti, J.; Marín, A.; Markert, C.; Marquard, M.; Martin, N. A.; Martin Blanco, J.; Martinengo, P.; Martínez, M. I.; Martínez García, G.; Martinez Pedreira, M.; Mas, A.; Masciocchi, S.; Masera, M.; Masoni, A.; Massacrier, L.; Mastroserio, A.; Matyja, A.; Mayer, C.; Mazer, J.; Mazzoni, M. A.; Mcdonald, D.; Meddi, F.; Melikyan, Y.; Menchaca-Rocha, A.; Meninno, E.; Mercado Pérez, J.; Meres, M.; Miake, Y.; Mieskolainen, M. M.; Mikhaylov, K.; Milano, L.; Milosevic, J.; Minervini, L. M.; Mischke, A.; Mishra, A. N.; Miskowiec, D.; Mitra, J.; Mitu, C. M.; Mohammadi, N.; Mohanty, B.; Molnar, L.; Montaño Zetina, L.; Montes, E.; Moreira De Godoy, D. A.; Moreno, L. A. P.; Moretto, S.; Morreale, A.; Morsch, A.; Muccifora, V.; Mudnic, E.; Mühlheim, D.; Muhuri, S.; Mukherjee, M.; Mulligan, J. D.; Munhoz, M. G.; Munzer, R. H.; Murray, S.; Musa, L.; Musinsky, J.; Naik, B.; Nair, R.; Nandi, B. K.; Nania, R.; Nappi, E.; Naru, M. U.; Natal da Luz, H.; Nattrass, C.; Nayak, K.; Nayak, T. K.; Nazarenko, S.; Nedosekin, A.; Nellen, L.; Ng, F.; Nicassio, M.; Niculescu, M.; Niedziela, J.; Nielsen, B. S.; Nikolaev, S.; Nikulin, S.; Nikulin, V.; Noferini, F.; Nomokonov, P.; Nooren, G.; Noris, J. C. C.; Norman, J.; Nyanin, A.; Nystrand, J.; Oeschler, H.; Oh, S.; Oh, S. K.; Ohlson, A.; Okatan, A.; Okubo, T.; Olah, L.; Oleniacz, J.; Oliveira Da Silva, A. C.; Oliver, M. H.; Onderwaater, J.; Oppedisano, C.; Orava, R.; Ortiz Velasquez, A.; Oskarsson, A.; Otwinowski, J.; Oyama, K.; Ozdemir, M.; Pachmayer, Y.; Pagano, P.; Paić, G.; Pal, S. K.; Pan, J.; Pandey, A. K.; Papcun, P.; Papikyan, V.; Pappalardo, G. S.; Pareek, P.; Park, W. J.; Parmar, S.; Passfeld, A.; Paticchio, V.; Patra, R. N.; Paul, B.; Peitzmann, T.; Pereira Da Costa, H.; Pereira De Oliveira Filho, E.; Peresunko, D.; Pérez Lara, C. E.; Perez Lezama, E.; Peskov, V.; Pestov, Y.; Petráček, V.; Petrov, V.; Petrovici, M.; Petta, C.; Piano, S.; Pikna, M.; Pillot, P.; Pinazza, O.; Pinsky, L.; Piyarathna, D. B.; Ploskon, M.; Planinic, M.; Pluta, J.; Pochybova, S.; Podesta-Lerma, P. L. M.; Poghosyan, M. G.; Polichtchouk, B.; Poljak, N.; Poonsawat, W.; Pop, A.; Porteboeuf-Houssais, S.; Porter, J.; Pospisil, J.; Prasad, S. K.; Preghenella, R.; Prino, F.; Pruneau, C. A.; Pshenichnov, I.; Puccio, M.; Puddu, G.; Pujahari, P.; Punin, V.; Putschke, J.; Qvigstad, H.; Rachevski, A.; Raha, S.; Rajput, S.; Rak, J.; Rakotozafindrabe, A.; Ramello, L.; Rami, F.; Raniwala, R.; Raniwala, S.; Räsänen, S. S.; Rascanu, B. T.; Rathee, D.; Read, K. F.; Redlich, K.; Reed, R. J.; Rehman, A.; Reichelt, P.; Reidt, F.; Ren, X.; Renfordt, R.; Reolon, A. R.; Reshetin, A.; Revol, J.-P.; Reygers, K.; Riabov, V.; Ricci, R. A.; Richert, T.; Richter, M.; Riedler, P.; Riegler, W.; Riggi, F.; Ristea, C.; Rocco, E.; Rodríguez Cahuantzi, M.; Rodriguez Manso, A.; Røed, K.; Rogochaya, E.; Rohr, D.; Röhrich, D.; Romita, R.; Ronchetti, F.; Ronflette, L.; Rosnet, P.; Rossi, A.; Roukoutakis, F.; Roy, A.; Roy, C.; Roy, P.; Rubio Montero, A. J.; Rui, R.; Russo, R.; Ryabinkin, E.; Ryabov, Y.; Rybicki, A.; Sadovsky, S.; Šafařík, K.; Sahlmuller, B.; Sahoo, P.; Sahoo, R.; Sahoo, S.; Sahu, P. K.; Saini, J.; Sakai, S.; Saleh, M. A.; Salzwedel, J.; Sambyal, S.; Samsonov, V.; Šándor, L.; Sandoval, A.; Sano, M.; Sarkar, D.; Scapparone, E.; Scarlassara, F.; Schiaua, C.; Schicker, R.; Schmidt, C.; Schmidt, H. R.; Schuchmann, S.; Schukraft, J.; Schulc, M.; Schuster, T.; Schutz, Y.; Schwarz, K.; Schweda, K.; Scioli, G.; Scomparin, E.; Scott, R.; Šefčík, M.; Seger, J. E.; Sekiguchi, Y.; Sekihata, D.; Selyuzhenkov, I.; Senosi, K.; Senyukov, S.; Serradilla, E.; Sevcenco, A.; Shabanov, A.; Shabetai, A.; Shadura, O.; Shahoyan, R.; Shangaraev, A.; Sharma, A.; Sharma, M.; Sharma, M.; Sharma, N.; Shigaki, K.; Shtejer, K.; Sibiriak, Y.; Siddhanta, S.; Sielewicz, K. M.; Siemiarczuk, T.; Silvermyr, D.; Silvestre, C.; Simatovic, G.; Simonetti, G.; Singaraju, R.; Singh, R.; Singha, S.; Singhal, V.; Sinha, B. C.; Sinha, T.; Sitar, B.; Sitta, M.; Skaali, T. B.; Slupecki, M.; Smirnov, N.; Snellings, R. J. M.; Snellman, T. W.; Søgaard, C.; Song, J.; Song, M.; Song, Z.; Soramel, F.; Sorensen, S.; Sozzi, F.; Spacek, M.; Spiriti, E.; Sputowska, I.; Spyropoulou-Stassinaki, M.; Stachel, J.; Stan, I.; Stefanek, G.; Stenlund, E.; Steyn, G.; Stiller, J. H.; Stocco, D.; Strmen, P.; Suaide, A. A. P.; Sugitate, T.; Suire, C.; Suleymanov, M.; Suljic, M.; Sultanov, R.; Šumbera, M.; Szabo, A.; Szanto de Toledo, A.; Szarka, I.; Szczepankiewicz, A.; Szymanski, M.; Tabassam, U.; Takahashi, J.; Tambave, G. J.; Tanaka, N.; Tangaro, M. A.; Tarhini, M.; Tariq, M.; Tarzila, M. G.; Tauro, A.; Tejeda Muñoz, G.; Telesca, A.; Terasaki, K.; Terrevoli, C.; Teyssier, B.; Thäder, J.; Thomas, D.; Tieulent, R.; Timmins, A. R.; Toia, A.; Trogolo, S.; Trombetta, G.; Trubnikov, V.; Trzaska, W. H.; Tsuji, T.; Tumkin, A.; Turrisi, R.; Tveter, T. S.; Ullaland, K.; Uras, A.; Usai, G. L.; Utrobicic, A.; Vajzer, M.; Vala, M.; Valencia Palomo, L.; Vallero, S.; Van Der Maarel, J.; Van Hoorne, J. W.; van Leeuwen, M.; Vanat, T.; Vande Vyvre, P.; Varga, D.; Vargas, A.; Vargyas, M.; Varma, R.; Vasileiou, M.; Vasiliev, A.; Vauthier, A.; Vechernin, V.; Veen, A. M.; Veldhoen, M.; Velure, A.; Venaruzzo, M.; Vercellin, E.; Vergara Limón, S.; Vernet, R.; Verweij, M.; Vickovic, L.; Viesti, G.; Viinikainen, J.; Vilakazi, Z.; Villalobos Baillie, O.; Villatoro Tello, A.; Vinogradov, A.; Vinogradov, L.; Vinogradov, Y.; Virgili, T.; Vislavicius, V.; Viyogi, Y. P.; Vodopyanov, A.; Völkl, M. A.; Voloshin, K.; Voloshin, S. A.; Volpe, G.; von Haller, B.; Vorobyev, I.; Vranic, D.; Vrláková, J.; Vulpescu, B.; Vyushin, A.; Wagner, B.; Wagner, J.; Wang, H.; Wang, M.; Watanabe, D.; Watanabe, Y.; Weber, M.; Weber, S. G.; Weiser, D. F.; Wessels, J. P.; Westerhoff, U.; Whitehead, A. M.; Wiechula, J.; Wikne, J.; Wilde, M.; Wilk, G.; Wilkinson, J.; Williams, M. C. S.; Windelband, B.; Winn, M.; Yaldo, C. G.; Yang, H.; Yang, P.; Yano, S.; Yasar, C.; Yin, Z.; Yokoyama, H.; Yoo, I.-K.; Yoon, J. H.; Yurchenko, V.; Yushmanov, I.; Zaborowska, A.; Zaccolo, V.; Zaman, A.; Zampolli, C.; Zanoli, H. J. C.; Zaporozhets, S.; Zardoshti, N.; Zarochentsev, A.; Závada, P.; Zaviyalov, N.; Zbroszczyk, H.; Zgura, I. S.; Zhalov, M.; Zhang, H.; Zhang, X.; Zhang, Y.; Zhang, C.; Zhang, Z.; Zhao, C.; Zhigareva, N.; Zhou, D.; Zhou, Y.; Zhou, Z.; Zhu, H.; Zhu, J.; Zichichi, A.; Zimmermann, A.; Zimmermann, M. B.; Zinovjev, G.; Zyzak, M.

2016-03-01

The production of prompt charmed mesons D0, D+ and D∗+, and their antiparticles, was measured with the ALICE detector in Pb-Pb collisions at the centre-of-mass energy per nucleon pair, sqrt{s_{NN}} , of 2 .76 TeV. The production yields for rapidity | y| < 0 .5 are presented as a function of transverse momentum, p T, in the interval 1-36 GeV /c for the centrality class 0-10% and in the interval 1-16 GeV /c for the centrality class 30-50%. The nuclear modification factor R AA was computed using a proton-proton reference at sqrt{s}=2.76 TeV, based on measurements at sqrt{s}=7 TeV and on theoretical calculations. A maximum suppression by a factor of 5-6 with respect to binary-scaled pp yields is observed for the most central collisions at p T of about 10 GeV /c. A suppression by a factor of about 2-3 persists at the highest p T covered by the measurements. At low p T (1-3 GeV /c), the R AA has large uncertainties that span the range 0.35 (factor of about 3 suppression) to 1 (no suppression). In all p T intervals, the R AA is larger in the 30-50% centrality class compared to central collisions. The D-meson R AA is also compared with that of charged pions and, at large p T, charged hadrons, and with model calculations. [Figure not available: see fulltext.

Field Test of a Three-Channel Seismic Event Discriminator

DTIC Science & Technology

1975-03-01

vault contains three corner piers, in addition to the primary central pier. Using the corner piers, a pair of 19-foot long-period mercury tiltmeters ...seismometers were the sensors used in testing the seismic event- discriminator system. The recording equipment consisted of an eight- channel pressure

PAIRED WATERSHED STUDY OF LAND-USE AND CLIMATE CHANGE IMPACT ON SMALL STREAMS

EPA Science Inventory

EPA installed flow monitoring stations on three tributaries to the Shepherd's Creek just outside of Cincinnati, Ohio. The western and central tributaries are on the urban fringe with headwaters derived from suburban storm water systems. The eastern tributary is entirely contain...

Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer

PubMed Central

Dršata, Tomáš; Pérez, Alberto; Orozco, Modesto; Morozov, Alexandre V.; Šponer, Jiřĺ; Lankaš, Filip

2013-01-01

The Dickerson–Drew dodecamer (DD) d-[CGCGAATTCGCG]2 is a prototypic B-DNA molecule whose sequence-specific structure and dynamics have been investigated by many experimental and computational studies. Here, we present an analysis of DD properties based on extensive atomistic molecular dynamics (MD) simulations using different ionic conditions and water models. The 0.6–2.4-µs-long MD trajectories are compared to modern crystallographic and NMR data. In the simulations, the duplex ends can adopt an alternative base-pairing, which influences the oligomer structure. A clear relationship between the BI/BII backbone substates and the basepair step conformation has been identified, extending previous findings and exposing an interesting structural polymorphism in the helix. For a given end pairing, distributions of the basepair step coordinates can be decomposed into Gaussian-like components associated with the BI/BII backbone states. The nonlocal stiffness matrices for a rigid-base mechanical model of DD are reported for the first time, suggesting salient stiffness features of the central A-tract. The Riemann distance and Kullback–Leibler divergence are used for stiffness matrix comparison. The basic structural parameters converge very well within 300 ns, convergence of the BI/BII populations and stiffness matrices is less sharp. Our work presents new findings about the DD structural dynamics, mechanical properties, and the coupling between basepair and backbone configurations, including their statistical reliability. The results may also be useful for optimizing future force fields for DNA. PMID:23976886

RNA Structural Analysis by Evolving SHAPE Chemistry

PubMed Central

Spitale, Robert C.; Flynn, Ryan A.; Torre, Eduardo A.; Kool, Eric T.; Chang, Howard Y.

2017-01-01

RNA is central to the flow of biological information. From transcription to splicing, RNA localization, translation, and decay, RNA is intimately involved in regulating every step of the gene expression program, and is thus essential for health and understanding disease. RNA has the unique ability to base-pair with itself and other nucleic acids to form complex structures. Hence the information content in RNA is not simply its linear sequence of bases, but is also encoded in complex folding of RNA molecules. A general chemical functionality that all RNAs have is a 2’-hydroxyl group in the ribose ring, and the reactivity of the 2'-hydroxyl in RNA is gated by local nucleotide flexibility. In other words, the 2'-hydroxyl is reactive at single-stranded and conformationally flexible positions but is unreactive at nucleotides constrained by base pairing. Recent efforts have been focused on developing reagents that modify RNA as a function of RNA 2’ hydroxyl group flexibility. Such RNA structure probing techniques can be read out by primer extension in experiments termed RNA SHAPE (Selective 2’ Hydroxyl Acylation and Primer Extension). Herein we describe the efforts devoted to the design and utilization of SHAPE probes for characterizing RNA structure. We also describe current technological advances that are being used to utilize SHAPE chemistry with deep sequencing to probe many RNAs in parallel. The merger of chemistry with genomics is sure to open the door to genome-wide exploration of RNA structure and function. PMID:25132067

A mechanical mechanism for translocation of ring-shaped helicases on DNA and its demonstration in a macroscopic simulation system

NASA Astrophysics Data System (ADS)

Chou, Y. C.

2018-04-01

The asymmetry in the two-layered ring structure of helicases and the random thermal fluctuations of the helicase and DNA molecules are considered as the bases for the generation of the force required for translocation of the ring-shaped helicase on DNA. The helicase comprises a channel at its center with two unequal ends, through which strands of DNA can pass. The random collisions between the portion of the DNA strand in the central channel and the wall of the channel generate an impulsive force toward the small end. This impulsive force is the starting point for the helicase to translocate along the DNA with the small end in front. Such a physical mechanism may serve as a complementary for the chemomechanical mechanism of the translocation of helicase on DNA. When the helicase arrives at the junction of ssDNA and dsDNA (a fork), the collision between the helicase and the closest base pair may produce a sufficient impulsive force to break the weak hydrogen bond of the base pair. Thus, the helicase may advance and repeat the process of unwinding the dsDNA strand. This mechanism was tested in a macroscopic simulation system where the helicase was simulated using a truncated-cone structure and DNA was simulated with bead chains. Many features of translocation and unwinding such as translocation on ssDNA and dsDNA, unwinding of dsDNA, rewinding, strand switching, and Holliday junction resolution were reproduced.

Synaptonemal Complex Components Persist at Centromeres and Are Required for Homologous Centromere Pairing in Mouse Spermatocytes

PubMed Central

Kouznetsova, Anna; Scherthan, Harry; Höög, Christer; Dawson, Dean S.; Pezza, Roberto J.

2012-01-01

Recent studies in simple model organisms have shown that centromere pairing is important for ensuring high-fidelity meiotic chromosome segregation. However, this process and the mechanisms regulating it in higher eukaryotes are unknown. Here we present the first detailed study of meiotic centromere pairing in mouse spermatogenesis and link it with key events of the G2/metaphase I transition. In mouse we observed no evidence of the persistent coupling of centromeres that has been observed in several model organisms. We do however find that telomeres associate in non-homologous pairs or small groups in B type spermatogonia and pre-leptotene spermatocytes, and this association is disrupted by deletion of the synaptonemal complex component SYCP3. Intriguingly, we found that, in mid prophase, chromosome synapsis is not initiated at centromeres, and centromeric regions are the last to pair in the zygotene-pachytene transition. In late prophase, we first identified the proteins that reside at paired centromeres. We found that components of the central and lateral element and transverse filaments of the synaptonemal complex are retained at paired centromeres after disassembly of the synaptonemal complex along diplotene chromosome arms. The absence of SYCP1 prevents centromere pairing in knockout mouse spermatocytes. The localization dynamics of SYCP1 and SYCP3 suggest that they play different roles in promoting homologous centromere pairing. SYCP1 remains only at paired centromeres coincident with the time at which some kinetochore proteins begin loading at centromeres, consistent with a role in assembly of meiosis-specific kinetochores. After removal of SYCP1 from centromeres, SYCP3 then accumulates at paired centromeres where it may promote bi-orientation of homologous centromeres. We propose that, in addition to their roles as synaptonemal complex components, SYCP1 and SYCP3 act at the centromeres to promote the establishment and/or maintenance of centromere pairing and, by doing so, improve the segregation fidelity of mammalian meiotic chromosomes. PMID:22761579

Electron-positron pairs, Compton reflection, and the X-ray spectra of active galactic nuclei

NASA Technical Reports Server (NTRS)

Zdziarski, Andrzej A.; Ghisellini, Gabriele; George, Ian M.; Fabian, A. C.; Svensson, Roland; Done, Chris

1990-01-01

It is shown here that reprocessing of radiation fron nonthermal pair cascades by cold material in the central parts of active galactic nuclei (AGN) gives rise to X-ray and gamma-ray spectra that satisfy current observational constraints. An average 1-30 keV X-ray spectral index alpha(x) of about 0.7 in the compact range 30-300 is obtained for a wide range of Lorentz factors of the injected electrons. The gamma-ray spectra are steep, with alpha(gamma) about two, and satisfy the observational constraints. Radiation from pair cascades exhibits steep power law decreases in soft X-rays similar to those observed in AGN. The overall picture is consistent with AGN having an accretion disk which intercepts and reprocesses a substantial fraction of the nonthermal continuum incident upon it from above and below.

Quasi-planar elemental clusters in pair interactions approximation

NASA Astrophysics Data System (ADS)

Chkhartishvili, Levan

2016-01-01

The pair-interactions approximation, when applied to describe elemental clusters, only takes into account bonding between neighboring atoms. According to this approach, isomers of wrapped forms of 2D clusters - nanotubular and fullerene-like structures - and truly 3D clusters, are generally expected to be more stable than their quasi-planar counterparts. This is because quasi-planar clusters contain more peripheral atoms with dangling bonds and, correspondingly, fewer atoms with saturated bonds. However, the differences in coordination numbers between central and peripheral atoms lead to the polarization of bonds. The related corrections to the molar binding energy can make small, quasi-planar clusters more stable than their 2D wrapped allotropes and 3D isomers. The present work provides a general theoretical frame for studying the relative stability of small elemental clusters within the pair interactions approximation.

Development and evaluation of a crowdsourcing methodology for knowledge base construction: identifying relationships between clinical problems and medications

PubMed Central

Wright, Adam; Laxmisan, Archana; Ottosen, Madelene J; McCoy, Jacob A; Butten, David; Sittig, Dean F

2012-01-01

Objective We describe a novel, crowdsourcing method for generating a knowledge base of problem–medication pairs that takes advantage of manually asserted links between medications and problems. Methods Through iterative review, we developed metrics to estimate the appropriateness of manually entered problem–medication links for inclusion in a knowledge base that can be used to infer previously unasserted links between problems and medications. Results Clinicians manually linked 231 223 medications (55.30% of prescribed medications) to problems within the electronic health record, generating 41 203 distinct problem–medication pairs, although not all were accurate. We developed methods to evaluate the accuracy of the pairs, and after limiting the pairs to those meeting an estimated 95% appropriateness threshold, 11 166 pairs remained. The pairs in the knowledge base accounted for 183 127 total links asserted (76.47% of all links). Retrospective application of the knowledge base linked 68 316 medications not previously linked by a clinician to an indicated problem (36.53% of unlinked medications). Expert review of the combined knowledge base, including inferred and manually linked problem–medication pairs, found a sensitivity of 65.8% and a specificity of 97.9%. Conclusion Crowdsourcing is an effective, inexpensive method for generating a knowledge base of problem–medication pairs that is automatically mapped to local terminologies, up-to-date, and reflective of local prescribing practices and trends. PMID:22582202

Acuity of a Cryptochrome and Vision-Based Magnetoreception System in Birds

PubMed Central

Solov'yov, Ilia A.; Mouritsen, Henrik; Schulten, Klaus

2010-01-01

Abstract The magnetic compass of birds is embedded in the visual system and it has been hypothesized that the primary sensory mechanism is based on a radical pair reaction. Previous models of magnetoreception have assumed that the radical pair-forming molecules are rigidly fixed in space, and this assumption has been a major objection to the suggested hypothesis. In this article, we investigate theoretically how much disorder is permitted for the radical pair-forming, protein-based magnetic compass in the eye to remain functional. Our study shows that only one rotational degree of freedom of the radical pair-forming protein needs to be partially constrained, while the other two rotational degrees of freedom do not impact the magnetoreceptive properties of the protein. The result implies that any membrane-associated protein is sufficiently restricted in its motion to function as a radical pair-based magnetoreceptor. We relate our theoretical findings to the cryptochromes, currently considered the likeliest candidate to furnish radical pair-based magnetoreception. PMID:20655831

Filter Paper-based Nucleic Acid Storage in High-throughput Solid Tumor Genotyping.

PubMed

Stachler, Matthew; Jia, Yonghui; Sharaf, Nematullah; Wade, Jacqueline; Longtine, Janina; Garcia, Elizabeth; Sholl, Lynette M

2015-01-01

Molecular testing of tumors from formalin-fixed paraffin-embedded (FFPE) tissue blocks is central to clinical practice; however, it requires histology support and increases test turnaround time. Prospective fresh frozen tissue collection requires special handling, additional storage space, and may not be feasible for small specimens. Filter paper-based collection of tumor DNA reduces the need for histology support, requires little storage space, and preserves high-quality nucleic acid. We investigated the performance of tumor smears on filter paper in solid tumor genotyping, as compared with paired FFPE samples. Whatman FTA Micro Card (FTA preps) smears were prepared from 21 fresh tumor samples. A corresponding cytology smear was used to assess tumor cellularity and necrosis. DNA was isolated from FTA preps and FFPE core samples using automated methods and quantified using SYBR green dsDNA detection. Samples were genotyped for 471 mutations on a mass spectrophotometry-based platform (Sequenom). DNA concentrations from FTA preps and FFPE correlated for untreated carcinomas but not for mesenchymal tumors (Spearman σ=0.39 and σ=-0.1, respectively). Average DNA concentrations were lower from FTA preps as compared with FFPE, but DNA quality was higher with less fragmentation. Seventy-six percent of FTA preps and 86% of FFPE samples generated adequate DNA for genotyping. FTA preps tended to perform poorly for collection of DNA from pretreated carcinomas and mesenchymal neoplasms. Of the 16 paired DNA samples that were genotyped, 15 (94%) gave entirely concordant results. Filter paper-based sample preservation is a feasible alternative to FFPE for use in automated, high-throughput genotyping of carcinomas.

A structural determinant in the uracil DNA glycosylase superfamily for the removal of uracil from adenine/uracil base pairs

PubMed Central

Lee, Dong-Hoon; Liu, Yinling; Lee, Hyun-Wook; Xia, Bo; Brice, Allyn R.; Park, Sung-Hyun; Balduf, Hunter; Dominy, Brian N.; Cao, Weiguo

2015-01-01

The uracil DNA glycosylase superfamily consists of several distinct families. Family 2 mismatch-specific uracil DNA glycosylase (MUG) from Escherichia coli is known to exhibit glycosylase activity on three mismatched base pairs, T/U, G/U and C/U. Family 1 uracil N-glycosylase (UNG) from E. coli is an extremely efficient enzyme that can remove uracil from any uracil-containing base pairs including the A/U base pair. Here, we report the identification of an important structural determinant that underlies the functional difference between MUG and UNG. Substitution of a Lys residue at position 68 with Asn in MUG not only accelerates the removal of uracil from mismatched base pairs but also enables the enzyme to gain catalytic activity on A/U base pairs. Binding and kinetic analysis demonstrate that the MUG-K68N substitution results in enhanced ground state binding and transition state interactions. Molecular modeling reveals that MUG-K68N, UNG-N123 and family 5 Thermus thermophiles UDGb-A111N can form bidentate hydrogen bonds with the N3 and O4 moieties of the uracil base. Genetic analysis indicates the gain of function for A/U base pairs allows the MUG-K68N mutant to remove uracil incorporated into the genome during DNA replication. The implications of this study in the origin of life are discussed. PMID:25550433

Structural features of the DNA hairpin d(ATCCTA-GTTA-TAGGAT): formation of a G-A base pair in the loop.

PubMed Central

van Dongen, M J; Mooren, M M; Willems, E F; van der Marel, G A; van Boom, J H; Wijmenga, S S; Hilbers, C W

1997-01-01

The three-dimensional structure of the hairpin formed by d(ATCCTA-GTTA-TAGGAT) has been determined by means of two-dimensional NMR studies, distance geometry and molecular dynamics calculations. The first and the last residues of the tetraloop of this hairpin form a sheared G-A base pair on top of the six Watson-Crick base pairs in the stem. The glycosidic torsion angles of the guanine and adenine residues in the G-A base pair reside in the anti and high- anti domain ( approximately -60 degrees ) respectively. Several dihedral angles in the loop adopt non-standard values to accommodate this base pair. The first and second residue in the loop are stacked in a more or less normal helical fashion; the fourth loop residue also stacks upon the stem, while the third residue is directed away from the loop region. The loop structure can be classified as a so-called type-I loop, in which the bases at the 5'-end of the loop stack in a continuous fashion. In this situation, loop stability is unlikely to depend heavily on the nature of the unpaired bases in the loop. Moreover, the present study indicates that the influence of the polarity of a closing A.T pair is much less significant than that of a closing C.G base pair. PMID:9092659

Solar dimming above temperate forests and its impact on local climate

NASA Astrophysics Data System (ADS)

Tudoroiu, M.; Genesio, L.; Gioli, B.; Schume, H.; Knohl, A.; Brümmer, C.; Miglietta, F.

2018-06-01

Vegetation has a substantial impact on the local climate. Land cover changes through afforestation or deforestation can amplify or mitigate climate warming by changes in biophysical and biogeochemical mechanisms. In the montane to subalpine area of the Eastern Alps in Europe, where forests have constantly expanded in the last four decades, data of meteorological stations show a consistent reduction in incoming global radiation for the period 2000–2015. To assess the potential role of forests in contributing to such a reduction, three site pairs in Central Europe with neighbouring forest and non-forest sites were analysed. In all the pairs, a lower amount of incoming radiation was recorded at the forest site. When biophysical mechanisms such as albedo, surface roughness and Bowen ratio changes were modelled together with changes in global radiation, the total radiative forcing accounted for a rate of change in air temperature was equal to 0.032 °C ± 0.01 °C per Wm‑2. These results suggest that local climate is influenced by land cover change through afforestation both via albedo and radiation feedbacks but also by means of indirect biophysical and species-dependent mechanisms. The data obtained for the site pairs in Central Europe are finally discussed to infer the occurrence of similar forest-driven effects in the Eastern Alps which may explain part of the solar dimming observed in high elevation weather stations.

Hydration of Watson-Crick base pairs and dehydration of Hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions.

PubMed

Miyoshi, Daisuke; Nakamura, Kaori; Tateishi-Karimata, Hisae; Ohmichi, Tatsuo; Sugimoto, Naoki

2009-03-18

It has been revealed recently that molecular crowding, which is one of the largest differences between in vivo and in vitro conditions, is a critical factor determining the structure, stability, and function of nucleic acids. However, the effects of molecular crowding on Watson-Crick and Hoogsteen base pairs remain unclear. In order to investigate directly and quantitatively the molecular crowding effects on base pair types in nucleic acids, we designed intramolecular parallel- and antiparallel-stranded DNA duplexes consisting of Hoogsteen and Watson-Crick base pairs, respectively, as well as an intramolecular parallel-stranded triplex containing both types of base pairs. Thermodynamic analyses demonstrated that the values of free energy change at 25 degrees C for Hoogsteen base-pair formations decreased from +1.45 +/- 0.15 to +1.09 +/- 0.13 kcal mol(-1), and from -1.89 +/- 0.13 to -2.71 +/- 0.11 kcal mol(-1) in the intramolecular duplex and triplex, respectively, when the concentration of PEG 200 (polyethylene glycol with average molecular weight 200) increased from 0 to 20 wt %. However, corresponding values for Watson-Crick formation in the duplex and triplex increased from -10.2 +/- 0.2 to -8.7 +/- 0.1 kcal mol(-1), and from -10.8 +/- 0.2 to -9.2 +/- 0.2 kcal mol(-1), respectively. Furthermore, it was revealed that the opposing effects of molecular crowding on the Hoogsteen and Watson-Crick base pairs were due to different behaviors of water molecules binding to the DNA strands.

Dietary patterns in India and their association with obesity and central obesity.

PubMed

Satija, Ambika; Hu, Frank B; Bowen, Liza; Bharathi, Ankalmadugu V; Vaz, Mario; Prabhakaran, Dorairaj; Reddy, K Srinath; Ben-Shlomo, Yoav; Davey Smith, George; Kinra, Sanjay; Ebrahim, Shah

2015-11-01

Obesity is a growing problem in India, the dietary determinants of which have been studied using an 'individual food/nutrient' approach. Examining dietary patterns may provide more coherent findings, but few studies in developing countries have adopted this approach. The present study aimed to identify dietary patterns in an Indian population and assess their relationship with anthropometric risk factors. FFQ data from the cross-sectional sib-pair Indian Migration Study (IMS; n 7067) were used to identify dietary patterns using principal component analysis. Mixed-effects logistic regression was used to examine associations with obesity and central obesity. The IMS was conducted at four factory locations across India: Lucknow, Nagpur, Hyderabad and Bangalore. The participants were rural-to-urban migrant and urban non-migrant factory workers, their rural and urban resident siblings, and their co-resident spouses. Three dietary patterns were identified: 'cereals-savoury foods' (cooked grains, rice/rice-based dishes, snacks, condiments, soups, nuts), 'fruit-veg-sweets-snacks' (Western cereals, vegetables, fruit, fruit juices, cooked milk products, snacks, sugars, sweets) and 'animal-food' (red meat, poultry, fish/seafood, eggs). In adjusted analysis, positive graded associations were found between the 'animal-food' pattern and both anthropometric risk factors. Moderate intake of the 'cereals-savoury foods' pattern was associated with reduced odds of obesity and central obesity. Distinct dietary patterns were identified in a large Indian sample, which were different from those identified in previous literature. A clear 'plant food-based/animal food-based pattern' dichotomy emerged, with the latter being associated with higher odds of anthropometric risk factors. Longitudinal studies are needed to further clarify this relationship in India.

Theory of nodal s ±-wave pairing symmetry in the Pu-based 115 superconductor family

DOE PAGES

Das, Tanmoy; Zhu, Jian -Xin; Graf, Matthias J.

2015-02-27

The spin-fluctuation mechanism of superconductivity usually results in the presence of gapless or nodal quasiparticle states in the excitation spectrum. Nodal quasiparticle states are well established in copper-oxide, and heavy-fermion superconductors, but not in iron-based superconductors. Here, we study the pairing symmetry and mechanism of a new class of plutonium-based high-T c superconductors and predict the presence of a nodal s⁺⁻ wave pairing symmetry in this family. Starting from a density-functional theory (DFT) based electronic structure calculation we predict several three-dimensional (3D) Fermi surfaces in this 115 superconductor family. We identify the dominant Fermi surface “hot-spots” in the inter-band scatteringmore » channel, which are aligned along the wavevector Q = (π, π, π), where degeneracy could induce sign-reversal of the pairing symmetry. Our calculation demonstrates that the s⁺⁻ wave pairing strength is stronger than the previously thought d-wave pairing; and more importantly, this pairing state allows for the existence of nodal quasiparticles. Finally, we predict the shape of the momentum- and energy-dependent magnetic resonance spectrum for the identification of this pairing symmetry.« less

Growth properties associated with A-U replacement of specific G-C base pairs in 16S rRNA from Escherichia coli.

PubMed Central

Triman, K L

1995-01-01

Mutations that disrupt each of seven specific G-C base pairs in 16S rRNA from Escherichia coli confer loss of expression of a plasmid-encoded 16S rRNA selectable marker (spectinomycin resistance). However, A-U replacement of G-C base pairs at nucleotides 359/52 or 1292/1245 in 16S rRNA permits normal expression of the marker. By contrast, A-U replacements at 146/176, 153/168, 350/339, or 1293/1244 are associated with loss of expression of the marker. These genetic studies are designed to determine the importance of specific base pairs by assessment of the structural and functional impairments of 16S rRNA molecules resulting from expression of base pair substitutions at these positions. PMID:7543481

The United States: A Persistent Debate

ERIC Educational Resources Information Center

van Scotter, Richard; Hartoonian, H. Michael; White, William E.; Davis, James E.

2007-01-01

American democratic society is sustained through debate among its citizens. Four sets of value tensions--(1) law versus ethics, (2) private wealth versus common wealth, (3) freedom versus equality, and (4) unity versus diversity--are central in allowing citizens to address matters of public interest through debate. These value pairs are the…

Development of Selective Attention in Reflective and Impulsive Children.

ERIC Educational Resources Information Center

Weiner, Alan S.; Berzonsky, Michael D.

Selective attention was assessed in second, fourth, and sixth grade reflective and impulsive children with an incidental learning task using pictures (animal-household object pairs) or shapes (colored forms) as stimuli. By the sixth grade, reflective children displayed less incidental learning and greater central learning than impulsive children…

Central Cannabinoid Receptors Modulate Acquisition of Eyeblink Conditioning

ERIC Educational Resources Information Center

Steinmetz, Adam B.; Freeman, John H.

2010-01-01

Delay eyeblink conditioning is established by paired presentations of a conditioned stimulus (CS) such as a tone or light, and an unconditioned stimulus (US) that elicits the blink reflex. Conditioned stimulus information is projected from the basilar pontine nuclei to the cerebellar interpositus nucleus and cortex. The cerebellar cortex,…

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

PubMed

Lee, Jie Hyun; Park, Heuk; Kang, Sae-Kyoung; Lee, Joon Ki; Chung, Hwan Seok

2015-11-30

In this study, we propose and experimentally demonstrate a wavelength domain rogue-free ONU based on wavelength-pairing of downstream and upstream signals for time/wavelength division-multiplexed optical access networks. The wavelength-pairing tunable filter is aligned to the upstream wavelength channel by aligning it to one of the downstream wavelength channels. Wavelength-pairing is implemented with a compact and cyclic Si-AWG integrated with a Ge-PD. The pairing filter covered four 100 GHz-spaced wavelength channels. The feasibility of the wavelength domain rogue-free operation is investigated by emulating malfunction of the misaligned laser. The wavelength-pairing tunable filter based on the Si-AWG blocks the upstream signal in the non-assigned wavelength channel before data collision with other ONUs.

Orbital selective pairing and gap structures of iron-based superconductors

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

Kreisel, Andreas; Andersen, Brian M.; Sprau, P. O.

We discuss the in uence on spin-fluctuation pairing theory of orbital selective strong correlation effects in Fe-based superconductors, particularly Fe chalcogenide systems. We propose that a key ingredient for an improved itinerant pairing theory is orbital selectivity, i.e., incorporating the reduced coherence of quasiparticles occupying specific orbital states. This modifies the usual spin-fluctuation via suppression of pair scattering processes involving those less coherent states and results in orbital selective Cooper pairing of electrons in the remaining states. We show that this paradigm yields remarkably good agreement with the experimentally observed anisotropic gap structures in both bulk and monolayer FeSe, asmore » well as LiFeAs, indicating that orbital selective Cooper pairing plays a key role in the more strongly correlated iron-based superconductors.« less

Orbital selective pairing and gap structures of iron-based superconductors

DOE PAGES

Kreisel, Andreas; Andersen, Brian M.; Sprau, P. O.; ...

2017-05-08

We discuss the in uence on spin-fluctuation pairing theory of orbital selective strong correlation effects in Fe-based superconductors, particularly Fe chalcogenide systems. We propose that a key ingredient for an improved itinerant pairing theory is orbital selectivity, i.e., incorporating the reduced coherence of quasiparticles occupying specific orbital states. This modifies the usual spin-fluctuation via suppression of pair scattering processes involving those less coherent states and results in orbital selective Cooper pairing of electrons in the remaining states. We show that this paradigm yields remarkably good agreement with the experimentally observed anisotropic gap structures in both bulk and monolayer FeSe, asmore » well as LiFeAs, indicating that orbital selective Cooper pairing plays a key role in the more strongly correlated iron-based superconductors.« less

Acid-induced exchange of the imino proton in G.C pairs.

PubMed Central

Nonin, S; Leroy, J L; Gueron, M

1996-01-01

Acid-induced catalysis of imino proton exchange in G.C pairs of DNA duplexes is surprisingly fast, being nearly as fast as for the isolated nucleoside, despite base-pair dissociation constants in the range of 10(-5) at neutral or basic pH. It is also observed in terminal G.C pairs of duplexes and in base pairs of drug-DNA complexes. We have measured imino proton exchange in deoxyguanosine and in the duplex (ATATAGATCTATAT) as a function of pH. We show that acid-induced exchange can be assigned to proton transfer from N7-protonated guanosine to cytidine in the open state of the pair. This is faster than transfer from neutral guanosine (the process of intrinsic catalysis previously characterized at neutral ph) due to the lower imino proton pK of the protonated form, 7.2 instead of 9.4. Other interpretations are excluded by a study of exchange catalysis by formiate and cytidine as exchange catalysts. The cross-over pH between the regimes of pH-independent and acid-induced exchange rates is more basic in the case of base pairs than in the mononucleoside, suggestive of an increase by one to two decades in the dissociation constant of the base pair upon N7 protonation of G. Acid-induced catalysis is much weaker in A.T base pairs, as expected in view of the low pK for protonation of thymidine. PMID:8604298

Acid-induced exchange of the imino proton in G.C pairs.

PubMed

Nonin, S; Leroy, J L; Gueron, M

1996-02-15

Acid-induced catalysis of imino proton exchange in G.C pairs of DNA duplexes is surprisingly fast, being nearly as fast as for the isolated nucleoside, despite base-pair dissociation constants in the range of 10(-5) at neutral or basic pH. It is also observed in terminal G.C pairs of duplexes and in base pairs of drug-DNA complexes. We have measured imino proton exchange in deoxyguanosine and in the duplex (ATATAGATCTATAT) as a function of pH. We show that acid-induced exchange can be assigned to proton transfer from N7-protonated guanosine to cytidine in the open state of the pair. This is faster than transfer from neutral guanosine (the process of intrinsic catalysis previously characterized at neutral ph) due to the lower imino proton pK of the protonated form, 7.2 instead of 9.4. Other interpretations are excluded by a study of exchange catalysis by formiate and cytidine as exchange catalysts. The cross-over pH between the regimes of pH-independent and acid-induced exchange rates is more basic in the case of base pairs than in the mononucleoside, suggestive of an increase by one to two decades in the dissociation constant of the base pair upon N7 protonation of G. Acid-induced catalysis is much weaker in A.T base pairs, as expected in view of the low pK for protonation of thymidine.

Surface Wave Tomography of South China Sea from Ambient Seismic Noise and Two-station Measurements

NASA Astrophysics Data System (ADS)

Liang, W.-T.; Gung, Y.-C.

2012-04-01

We have taken the cross-correlation of seismic ambient noise technique as well as the two-station method to analyze the velocity structure in the South China Sea region. The dataset used in this study includes broadband waveforms recorded at the Taiwan BATS (Broadband Array in Taiwan for Seismology), Japan OHP (Ocean Hemisphere Project), Malaysia and Vietnam seismic networks. We remove the instrument response from daily data and filter the waveform with various frequency bands according to the length of each station-pair. Then we apply the commonly used 1-bit normalization to minimize the effect of earthquakes, instrumental irregularities, and non-stationary noise sources near to the stations. With the derived daily cross correlation function (CCF), we are able to examine the timing quality for each station-pair. We then obtain the surface Rayleigh wave dispersion curves from the stacked CCF for each station-pair. To cover the longer period band in the dispersion curves, we adopt the two-station method to compute both the group and phase velocities of surface waves. A new surface wave tomography based on ambient seismic noise study and traditional two-station technique has been achieved in this study. Raypaths that travel through the Central basin present higher velocity, which is in agreement with the idea of thin crust. On the other hand, the slower velocity between Taiwan and Northern Luzon, Philippine is mainly due to a thick accretionary prism above the Manila trench.

Rapid genotyping assays for the 4-base pair deletion of canine MDR1/ABCB1 gene and low frequency of the mutant allele in Border Collie dogs.

PubMed

Mizukami, Keijiro; Chang, Hye-Sook; Yabuki, Akira; Kawamichi, Takuji; Hossain, Mohammad A; Rahman, Mohammad M; Uddin, Mohammad M; Yamato, Osamu

2012-01-01

P-glycoprotein, encoded by the MDR1 or ABCB1 gene, is an integral component of the blood-brain barrier as an efflux pump for xenobiotics crucial in limiting drug uptake into the central nervous system. Dogs homozygous for a 4-base pair deletion of the canine MDR1 gene show altered expression or function of P-glycoprotein, resulting in neurotoxicosis after administration of the substrate drugs. In the present study, the usefulness of microchip electrophoresis for genotyping assays detecting this deletion mutation was evaluated. Mutagenically separated polymerase chain reaction (MS-PCR) and real-time PCR assays were newly developed and evaluated. Furthermore, a genotyping survey was carried out in a population of Border Collies dogs in Japan to determine the allele frequency in this breed. Microchip electrophoresis showed advantages in detection sensitivity and time saving over other modes of electrophoresis. The MS-PCR assay clearly discriminated all genotypes. Real-time PCR assay was most suitable for a large-scale survey due to its high throughput and rapidity. The genotyping survey demonstrated that the carrier and mutant allele frequencies were 0.49% and 0.25%, respectively, suggesting that the mutant allele frequency in Border Collies is markedly low compared to that in the susceptible dog breeds such as rough and smooth Collies.

Neuromuscular control of the point to point and oscillatory movements of a sagittal arm with the actor-critic reinforcement learning method.

PubMed

Golkhou, Vahid; Parnianpour, Mohamad; Lucas, Caro

2005-04-01

In this study, we have used a single link system with a pair of muscles that are excited with alpha and gamma signals to achieve both point to point and oscillatory movements with variable amplitude and frequency.The system is highly nonlinear in all its physical and physiological attributes. The major physiological characteristics of this system are simultaneous activation of a pair of nonlinear muscle-like-actuators for control purposes, existence of nonlinear spindle-like sensors and Golgi tendon organ-like sensor, actions of gravity and external loading. Transmission delays are included in the afferent and efferent neural paths to account for a more accurate representation of the reflex loops.A reinforcement learning method with an actor-critic (AC) architecture instead of middle and low level of central nervous system (CNS), is used to track a desired trajectory. The actor in this structure is a two layer feedforward neural network and the critic is a model of the cerebellum. The critic is trained by state-action-reward-state-action (SARSA) method. The critic will train the actor by supervisory learning based on the prior experiences. Simulation studies of oscillatory movements based on the proposed algorithm demonstrate excellent tracking capability and after 280 epochs the RMS error for position and velocity profiles were 0.02, 0.04 rad and rad/s, respectively.

Developing Topological Insulator Fiber Based Photon Pairs Source for Ultrafast Optoelectronic Applications

DTIC Science & Technology

2016-04-01

DEVELOPING TOPOLOGICAL INSULATOR FIBER BASED PHOTON PAIRS SOURCE FOR ULTRAFAST OPTOELECTRONIC APPLICATIONS NORTHWESTERN UNIVERSITY...REPORT TYPE FINAL TECHNICAL REPORT 3. DATES COVERED (From - To) APRIL 2015 – DEC 2015 4. TITLE AND SUBTITLE DEVELOPING TOPOLOGICAL INSULATOR FIBER BASED...in developing a new source for the production of correlated/entangled photon pairs based on the unique nanolayer properties of topological insulator

Impact of the structural integrity of the three-way junction of adenovirus VAI RNA on PKR inhibition

PubMed Central

Dzananovic, Edis; Astha; Chojnowski, Grzegorz; Deo, Soumya; Booy, Evan P.; Padilla-Meier, Pauline; McEleney, Kevin; Bujnicki, Janusz M.; McKenna, Sean A.

2017-01-01

Highly structured RNA derived from viral genomes is a key cellular indicator of viral infection. In response, cells produce the interferon inducible RNA-dependent protein kinase (PKR) that, when bound to viral dsRNA, phosphorylates eukaryotic initiation factor 2α and attenuates viral protein translation. Adenovirus can evade this line of defence through transcription of a non-coding RNA, VAI, an inhibitor of PKR. VAI consists of three base-paired regions that meet at a three-way junction; an apical stem responsible for the interaction with PKR, a central stem required for inhibition, and a terminal stem. Recent studies have highlighted the potential importance of the tertiary structure of the three-way junction to PKR inhibition by enabling interaction between regions of the central and terminal stems. To further investigate the role of the three-way junction, we characterized the binding affinity and inhibitory potential of central stem mutants designed to introduce subtle alterations. These results were then correlated with small-angle X-ray scattering solution studies and computational tertiary structural models. Our results demonstrate that while mutations to the central stem have no observable effect on binding affinity to PKR, mutations that appear to disrupt the structure of the three-way junction prevent inhibition of PKR. Therefore, we propose that instead of simply sequestering PKR, a specific structural conformation of the PKR-VAI complex may be required for inhibition. PMID:29053745

Color pattern analysis of nymphalid butterfly wings: revision of the nymphalid groundplan.

PubMed

Otaki, Joji M

2012-09-01

To better understand the developmental mechanisms of color pattern variation in butterfly wings, it is important to construct an accurate representation of pattern elements, known as the "nymphalid groundplan". However, some aspects of the current groundplan remain elusive. Here, I examined wing-wide elemental patterns of various nymphalid butterflies and confirmed that wing-wide color patterns are composed of the border, central, and basal symmetry systems. The central and basal symmetry systems can express circular patterns resembling eyespots, indicating that these systems have developmental mechanisms similar to those of the border symmetry system. The wing root band commonly occurs as a distinct symmetry system independent from the basal symmetry system. In addition, the marginal and submarginal bands are likely generated as a single system, referred to as the "marginal band system". Background spaces between two symmetry systems are sometimes light in coloration and can produce white bands, contributing significantly to color pattern diversity. When an element is enlarged with a pale central area, a visually similar (yet developmentally distinct) white band is produced. Based on the symmetric relationships of elements, I propose that both the central and border symmetry systems are comprised of "core elements" (the discal spot and the border ocelli, respectively) and a pair of "paracore elements" (the distal and proximal bands and the parafocal elements, respectively). Both core and paracore elements can be doubled, or outlined. Developmentally, this system configuration is consistent with the induction model, but not with the concentration gradient model for positional information.

Sensitivity to structure in action sequences: An infant event-related potential study.

PubMed

Monroy, Claire D; Gerson, Sarah A; Domínguez-Martínez, Estefanía; Kaduk, Katharina; Hunnius, Sabine; Reid, Vincent

2017-05-06

Infants are sensitive to structure and patterns within continuous streams of sensory input. This sensitivity relies on statistical learning, the ability to detect predictable regularities in spatial and temporal sequences. Recent evidence has shown that infants can detect statistical regularities in action sequences they observe, but little is known about the neural process that give rise to this ability. In the current experiment, we combined electroencephalography (EEG) with eye-tracking to identify electrophysiological markers that indicate whether 8-11-month-old infants detect violations to learned regularities in action sequences, and to relate these markers to behavioral measures of anticipation during learning. In a learning phase, infants observed an actor performing a sequence featuring two deterministic pairs embedded within an otherwise random sequence. Thus, the first action of each pair was predictive of what would occur next. One of the pairs caused an action-effect, whereas the second did not. In a subsequent test phase, infants observed another sequence that included deviant pairs, violating the previously observed action pairs. Event-related potential (ERP) responses were analyzed and compared between the deviant and the original action pairs. Findings reveal that infants demonstrated a greater Negative central (Nc) ERP response to the deviant actions for the pair that caused the action-effect, which was consistent with their visual anticipations during the learning phase. Findings are discussed in terms of the neural and behavioral processes underlying perception and learning of structured action sequences. Copyright © 2017 Elsevier Ltd. All rights reserved.

Interaction of paired cortical and peripheral nerve stimulation on human motor neurons.

PubMed

Poon, David E; Roy, Francois D; Gorassini, Monica A; Stein, Richard B

2008-06-01

This paper contrasts responses in the soleus muscle of normal human subjects to two major inputs: the tibial nerve (TN) and the corticospinal tract. Paired transcranial magnetic stimulation (TMS) of the motor cortex at intervals of 10-25 ms strongly facilitated the motor evoked potential (MEP) produced by the second stimulus. In contrast, paired TN stimulation produced a depression of the reflex response to the second stimulus. Direct activation of the pyramidal tract did not facilitate a second response, suggesting that the MEP facilitation observed using paired TMS occurred in the cortex. A TN stimulus also depressed a subsequent MEP. Since the TN stimulus depressed both inputs, the mechanism is probably post-synaptic, such as afterhyperpolarization of motor neurons. Presynaptic mechanisms, such as homosynaptic depression, would only affect the pathway used as a conditioning stimulus. When TN and TMS pulses were paired, the largest facilitation occurred when TMS preceded TN by about 5 ms, which is optimal for summation of the two pathways at the level of the spinal motor neurons. A later, smaller facilitation occurred when a single TN stimulus preceded TMS by 50-60 ms, an interval that allows enough time for the sensory afferent input to reach the sensory cortex and be relayed to the motor cortex. Other work indicates that repetitively pairing nerve stimuli and TMS at these intervals, known as paired associative stimulation, produces long-term increases in the MEP and may be useful in strengthening residual pathways after damage to the central nervous system.

Base pairing among three cis-acting sequences contributes to template switching during hepadnavirus reverse transcription.

PubMed

Liu, Ning; Tian, Ru; Loeb, Daniel D

2003-02-18

Synthesis of the relaxed-circular (RC) DNA genome of hepadnaviruses requires two template switches during plus-strand DNA synthesis: primer translocation and circularization. Although primer translocation and circularization use different donor and acceptor sequences, and are distinct temporally, they share the common theme of switching from one end of the minus-strand template to the other end. Studies of duck hepatitis B virus have indicated that, in addition to the donor and acceptor sequences, three other cis-acting sequences, named 3E, M, and 5E, are required for the synthesis of RC DNA by contributing to primer translocation and circularization. The mechanism by which 3E, M, and 5E act was not known. We present evidence that these sequences function by base pairing with each other within the minus-strand template. 3E base-pairs with one portion of M (M3) and 5E base-pairs with an adjacent portion of M (M5). We found that disrupting base pairing between 3E and M3 and between 5E and M5 inhibited primer translocation and circularization. More importantly, restoring base pairing with mutant sequences restored the production of RC DNA. These results are consistent with the model that, within duck hepatitis B virus capsids, the ends of the minus-strand template are juxtaposed via base pairing to facilitate the two template switches during plus-strand DNA synthesis.

Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif.

PubMed

Cojocaru, Vlad; Klement, Reinhard; Jovin, Thomas M

2005-01-01

Upon binding to the 15.5K protein, two tandem-sheared G-A base pairs are formed in the internal loop of the kink-turn motif of U4 snRNA (Kt-U4). We have reported that the folding of Kt-U4 is assisted by protein binding. Unstable interactions that contribute to a large opening of the free RNA ('k-e motion') were identified using locally enhanced sampling molecular dynamics simulations, results that agree with experiments. A detailed analysis of the simulations reveals that the k-e motion in Kt-U4 is triggered both by loss of G-A base pairs in the internal loop and backbone flexibility in the stems. Essential dynamics show that the loss of G-A base pairs is correlated along the first mode but anti-correlated along the third mode with the k-e motion. Moreover, when enhanced sampling was confined to the internal loop, the RNA adopted an alternative conformation characterized by a sharper kink, opening of G-A base pairs and modified stacking interactions. Thus, loss of G-A base pairs is insufficient for achieving a large opening of the free RNA. These findings, supported by previously published RNA structure probing experiments, suggest that G-A base pair formation occurs upon protein binding, thereby stabilizing a selective orientation of the stems.

The utilization of Nimbus-7 SMMR measurements to delineate rainfall over land

NASA Technical Reports Server (NTRS)

Rogers, E.; Siddalingaiah, H.

1982-01-01

Based on previous theoretical calculations, an empirical statistical approach to use satellite multifrequency dual polarized passive microwave data to detect rainfall areas over land was initiated. The addition of information from a lower frequency channel (18.0 or 10.7 GHz) was shown to improve the discrimination of rain from wet ground achieved by using a single frequency dual polarized (37 GHz) channel alone. The algorithm was developed and independently tested using data from the Nimbus-7 Scanning Multichannel Microwave Radiometer. Horizontally and vertically polarized brightness temperature pairs at 37, 18, 10.7 GHz were sampled for raining areas over land (determined from ground base radar), wet ground areas (adjacent and upwind from rain areas determined from radar), and dry land regions (areas where rain had not fallen in a 24h period) over the central and eastern United States. Surface thermodynamic temperatures were both above and below 15 deg C.

A High-Authority/Low-Authority Control Strategy for Coupled Aircraft-Style Bays

NASA Technical Reports Server (NTRS)

Schiller, N. H.; Fuller, C. R.; Cabell, R. H.

2006-01-01

This paper presents a numerical investigation of an active structural acoustic control strategy for coupled aircraft-style bays. While structural coupling can destabilize or limit the performance of some model-based decentralized control systems, fullycoupled centralized control strategies are impractical for typical aircraft containing several hundred bays. An alternative is to use classical rate feedback with matched, collocated transducer pairs to achieve active damping. Unfortunately, due to the conservative nature of this strategy, stability is guaranteed at the expense of achievable noise reduction. Therefore, this paper describes the development of a combined control strategy using robust active damping in addition to a high-authority controller based on linear quadratic Gaussian (LQG) theory. The combined control system is evaluated on a tensioned, two-bay model using piezoceramic actuators and ideal point velocity sensors. Transducer placement on the two-bay structure is discussed, and the advantages of a combined control strategy are presented.

A multiplexable TALE-based binary expression system for in vivo cellular interaction studies.

PubMed

Toegel, Markus; Azzam, Ghows; Lee, Eunice Y; Knapp, David J H F; Tan, Ying; Fa, Ming; Fulga, Tudor A

2017-11-21

Binary expression systems have revolutionised genetic research by enabling delivery of loss-of-function and gain-of-function transgenes with precise spatial-temporal resolution in vivo. However, at present, each existing platform relies on a defined exogenous transcription activator capable of binding a unique recognition sequence. Consequently, none of these technologies alone can be used to simultaneously target different tissues or cell types in the same organism. Here, we report a modular system based on programmable transcription activator-like effector (TALE) proteins, which enables parallel expression of multiple transgenes in spatially distinct tissues in vivo. Using endogenous enhancers coupled to TALE drivers, we demonstrate multiplexed orthogonal activation of several transgenes carrying cognate variable activating sequences (VAS) in distinct neighbouring cell types of the Drosophila central nervous system. Since the number of combinatorial TALE-VAS pairs is virtually unlimited, this platform provides an experimental framework for highly complex genetic manipulation studies in vivo.

Identification of a new Apscaviroid from Japanese persimmon.

PubMed

Nakaune, Ryoji; Nakano, Masaaki

2008-01-01

Three viroid-like sequences were detected from Japanese persimmon (Diospyrus kaki Thunb.) by RT-PCR using primers specific for members of the genus Apscaviroid. Based on the sequences, we determined the complete genomic sequences. Two had 92.1-94.3% sequence identity with citrus viroid OS (CVd-OS) and 91.4-96.3% identity with apple fruit crinkle viroid (AFCVd), respectively. Another one, tentatively named persimmon viroid (PVd), had 396 nucleotides and less than 70% sequence identity with known viroids. The secondary structure of PVd is proposed to be rod-like with extensive base pairing and contains the terminal conserved region and the central conserved region characteristic of the genus Apscaviroid. Moreover, we confirmed that the viroids, including PVd, are graft transmissible from persimmon to persimmon and that persimmon is a natural host of these viroids. According to its molecular and biological properties, PVd should be considered a member of a new species in the genus Apscaviroid.

Discrimination among individual Watson–Crick base pairs at the termini of single DNA hairpin molecules

PubMed Central

Vercoutere, Wenonah A.; Winters-Hilt, Stephen; DeGuzman, Veronica S.; Deamer, David; Ridino, Sam E.; Rodgers, Joseph T.; Olsen, Hugh E.; Marziali, Andre; Akeson, Mark

2003-01-01

Nanoscale α-hemolysin pores can be used to analyze individual DNA or RNA molecules. Serial examination of hundreds to thousands of molecules per minute is possible using ionic current impedance as the measured property. In a recent report, we showed that a nanopore device coupled with machine learning algorithms could automatically discriminate among the four combinations of Watson–Crick base pairs and their orientations at the ends of individual DNA hairpin molecules. Here we use kinetic analysis to demonstrate that ionic current signatures caused by these hairpin molecules depend on the number of hydrogen bonds within the terminal base pair, stacking between the terminal base pair and its nearest neighbor, and 5′ versus 3′ orientation of the terminal bases independent of their nearest neighbors. This report constitutes evidence that single Watson–Crick base pairs can be identified within individual unmodified DNA hairpin molecules based on their dynamic behavior in a nanoscale pore. PMID:12582251

[Mass spectrometric and quantum chemical study of dimeric associates of nucleosides].

PubMed

Sukhodub, L F; Aksenov, S A; Boldeskul, A I

1995-01-01

Deoxyribonucleosides H-bonded pairs were investigated using fast atom bombardment mass spectrometry and MNDO/H quantum chemistry method. It was shown that "rare" (enol or imin) forms of the nitrogen bases could form pairs with energy comparable with "canonical" base pair energy. It was shown that pair stability rows, which are measured using different experimental techniques, were in conformity each with other.

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

NASA Astrophysics Data System (ADS)

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

2016-05-01

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

Ultrabroadband phased-array radio frequency (RF) receivers based on optical techniques

NASA Astrophysics Data System (ADS)

Overmiller, Brock M.; Schuetz, Christopher A.; Schneider, Garrett; Murakowski, Janusz; Prather, Dennis W.

2014-03-01

Military operations require the ability to locate and identify electronic emissions in the battlefield environment. However, recent developments in radio detection and ranging (RADAR) and communications technology are making it harder to effectively identify such emissions. Phased array systems aid in discriminating emitters in the scene by virtue of their relatively high-gain beam steering and nulling capabilities. For the purpose of locating emitters, we present an approach realize a broadband receiver based on optical processing techniques applied to the response of detectors in conformal antenna arrays. This approach utilizes photonic techniques that enable us to capture, route, and process the incoming signals. Optical modulators convert the incoming signals up to and exceeding 110 GHz with appreciable conversion efficiency and route these signals via fiber optics to a central processing location. This central processor consists of a closed loop phase control system which compensates for phase fluctuations induced on the fibers due to thermal or acoustic vibrations as well as an optical heterodyne approach for signal conversion down to baseband. Our optical heterodyne approach uses injection-locked paired optical sources to perform heterodyne downconversion/frequency identification of the detected emission. Preliminary geolocation and frequency identification testing of electronic emissions has been performed demonstrating the capabilities of our RF receiver.

Twin hydroxymethyluracil-A base pair steps define the binding site for the DNA-binding protein TF1.

PubMed

Grove, A; Figueiredo, M L; Galeone, A; Mayol, L; Geiduschek, E P

1997-05-16

The DNA-bending protein TF1 is the Bacillus subtilis bacteriophage SPO1-encoded homolog of the bacterial HU proteins and the Escherichia coli integration host factor. We recently proposed that TF1, which binds with high affinity (Kd was approximately 3 nM) to preferred sites within the hydroxymethyluracil (hmU)-containing phage genome, identifies its binding sites based on sequence-dependent DNA flexibility. Here, we show that two hmU-A base pair steps coinciding with two previously proposed sites of DNA distortion are critical for complex formation. The affinity of TF1 is reduced 10-fold when both of these hmU-A base pair steps are replaced with A-hmU, G-C, or C-G steps; only modest changes in affinity result when substitutions are made at other base pairs of the TF1 binding site. Replacement of all hmU residues with thymine decreases the affinity of TF1 greatly; remarkably, the high affinity is restored when the two hmU-A base pair steps corresponding to previously suggested sites of distortion are reintroduced into otherwise T-containing DNA. T-DNA constructs with 3-base bulges spaced apart by 9 base pairs of duplex also generate nM affinity of TF1. We suggest that twin hmU-A base pair steps located at the proposed sites of distortion are key to target site selection by TF1 and that recognition is based largely, if not entirely, on sequence-dependent DNA flexibility.

[Trial manufacture of subsidiary tool and use of technique for shoulder joint of "Scapula Y"].

PubMed

Maejima, Hideyuki; Okamoto, Takahide; Yamazaki, Norihito; Hiyoshi, Kan; Tanaka, Tamotsu; Mori, Takeshi; Ako, Toshitaka; Ogawa, Norihisa

2002-07-01

The technique of "Scapula Y " is effective for capturing forward/backward dislocation of the humeral head and variation in surgical spine fracture. It is also indispensable for describing images of ossification at the tendon plate of the lower lobe of the acrominon and impingement syndrome. However, owing to large individual variations in body shape and position and shape of the scapula, the conventional method does not lend itself to stable reproduction of position or provide adequate diagnostic information. We measured the central angle of entry from scapula m24 pairs of dried bone (Indian) into the spine of the scapula from horizontal and forehead planes to determine the range of variation together with the clinical data referred to in the next paragraph. We then manufactured a trial subsidiary tool to set the angle of the central entering beam base on the acrominon to the spine of the scapula using data on measured angle from 50 clinical radiographs. We identified improvement in radiography of the scapula by using the subsidiary tool designed and manufactured on the basis of the above measured data.

Applied Meteorology Unit (AMU) Quarterly Report Third Quarter FY · 13

NASA Technical Reports Server (NTRS)

Bauman, William; Crawford, Winifred; Watson, Leela; Shafer, Jaclyn; Huddleston, Lisa

2013-01-01

The AMU team worked on seven tasks for their customers: (1) Ms. Crawford completed the objective lightning forecast tool for east -central Florida airports and delivered the tool and the final report to the customers. (2) Ms. Shafer continued work for Vandenberg Air Force Base on an automated tool to relate pressure gradients to peak winds. (3) Dr. Huddleston updated and delivered the tool that shows statistics on the timing of the first lightning strike of the day in the Kennedy Space Center (KSC)/Cape Canaveral Air Force Station (CCAFS) area. (4) Dr. Bauman continued work on a severe weather forecast tool focused on the Eastern Range (ER). (5) Ms. Crawford acquired the software and radar data needed to create a dual-Doppler analysis over the east-central Florida and KSC/CCAFS areas. (6) Mr. Decker continued developing a wind pairs database for the Launch Services Program to use when evaluating upper-level winds for launch vehicles. (7) Dr. Watson continued work to assimilate observational data into the high-resolution model configurations she created for Wallops Flight Facility and the ER.

Effects of selective excitotoxic lesions of the nucleus accumbens core, anterior cingulate cortex, and central nucleus of the amygdala on autoshaping performance in rats.

PubMed

Cardinal, Rudolf N; Parkinson, John A; Lachenal, Guillaume; Halkerston, Katherine M; Rudarakanchana, Nung; Hall, Jeremy; Morrison, Caroline H; Howes, Simon R; Robbins, Trevor W; Everitt, Barry J

2002-08-01

The nucleus accumbens core (AcbC), anterior cingulate cortex (ACC), and central nucleus of the amygdala (CeA) are required for normal acquisition of tasks based on stimulus-reward associations. However, it is not known whether they are involved purely in the learning process or are required for behavioral expression of a learned response. Rats were trained preoperatively on a Pavlovian autoshaping task in which pairing a visual conditioned stimulus (CS+) with food causes subjects to approach the CS+ while not approaching an unpaired stimulus (CS-). Subjects then received lesions of the AcbC, ACC, or CeA before being retested. AcbC lesions severely impaired performance; lesioned subjects approached the CS+ significantly less often than controls, failing to discriminate between the CS+ and CS-. ACC lesions also impaired performance but did not abolish discrimination entirely. CeA lesions had no effect on performance. Thus, the CeA is required for learning, but not expression, of a conditioned approach response, implying that it makes a specific contribution to the learning of stimulus-reward associations.

Understanding the kinetic mechanism of RNA single base pair formation

PubMed Central

Xu, Xiaojun; Yu, Tao; Chen, Shi-Jie

2016-01-01

RNA functions are intrinsically tied to folding kinetics. The most elementary step in RNA folding is the closing and opening of a base pair. Understanding this elementary rate process is the basis for RNA folding kinetics studies. Previous studies mostly focused on the unfolding of base pairs. Here, based on a hybrid approach, we investigate the folding process at level of single base pairing/stacking. The study, which integrates molecular dynamics simulation, kinetic Monte Carlo simulation, and master equation methods, uncovers two alternative dominant pathways: Starting from the unfolded state, the nucleotide backbone first folds to the native conformation, followed by subsequent adjustment of the base conformation. During the base conformational rearrangement, the backbone either retains the native conformation or switches to nonnative conformations in order to lower the kinetic barrier for base rearrangement. The method enables quantification of kinetic partitioning among the different pathways. Moreover, the simulation reveals several intriguing ion binding/dissociation signatures for the conformational changes. Our approach may be useful for developing a base pair opening/closing rate model. PMID:26699466

Comparison of Fingerprint and Iris Biometric Authentication for Control of Digital Signatures

PubMed Central

Zuckerman, Alan E.; Moon, Kenneth A.; Eaddy, Kenneth

2002-01-01

Biometric authentication systems can be used to control digital signature of medical documents. This pilot study evaluated the use of two different fingerprint technologies and one iris technology to control creation of digital signatures on a central server using public private key pairs stored on the server. Documents and signatures were stored in XML for portability. Key pairs and authentication certificates were generated during biometric enrollment. Usability and user acceptance were guarded and limitations of biometric systems prevented use of the system with all test subjects. The system detected alternations in the data content and provided future signer re-authentication for non-repudiation.

Coherent e+e- production at very low transverse momentum at STAR

NASA Astrophysics Data System (ADS)

Yang, Chi

2018-02-01

We report the measurements of e+e- pair production at very low e+e- pair transverse momentum (pT < 0.15 GeV/c) in Au+Au collisions at = 200 GeV and U+U collisions at = 193 GeV using the STAR detector at the Relativistic Heavy Ion Collider. In 60-80% centrality, significant excesses are observed with respect to hadronic cocktails in both Au+Au and U+U collisions. These excess yields can not be explained by a theoretical model calculation incorporating in-medium broadened ρ spectral function. Additionally, the distribution for excess yield is shown and found to be exponential at very low pT.

An ERP study of passive creative conceptual expansion using a modified alternate uses task.

PubMed

Kröger, Sören; Rutter, Barbara; Hill, Holger; Windmann, Sabine; Hermann, Christiane; Abraham, Anna

2013-08-21

A novel ERP paradigm was employed to investigate conceptual expansion, a central component of creative thinking. Participants were presented with word pairs, consisting of everyday objects and uses for these objects, which had to be judged based on the two defining criteria of creative products: unusualness and appropriateness. Three subject-determined trial types resulted from this judgement: high unusual and low appropriate (nonsensical uses), low unusual and high appropriate (common uses), and high unusual and high appropriate (creative uses). Word pairs of the creative uses type are held to passively induce conceptual expansion. The N400 component was not specifically modulated by conceptual expansion but was, instead, generally responsive as a function of unusualness or novelty of the stimuli (nonsense=creative>common). Explorative analyses in a later time window (500-900 ms) revealed that ERP activity in this phase indexes appropriateness (nonsense>creative=common). In the discussion of these findings with reference to the literature on semantic cognition, both components are proposed as indexing processes relevant to conceptual expansion as they are selectively involved in the encoding and integration of a newly established semantic connection between two previously unrelated concepts. Copyright © 2013 Elsevier B.V. All rights reserved.

Imino proton exchange and base-pair kinetics in the AMP-RNA aptamer complex.

PubMed

Nonin, S; Jiang, F; Patel, D J

1997-05-02

We report on the dynamics of base-pair opening in the ATP-binding asymmetric internal loop and flanking base-pairs of the AMP-RNA aptamer complex by monitoring the exchange characteristics of the extremely well resolved imino protons in the NMR spectrum of the complex. The kinetics of imino proton exchange as a function of basic pH or added ammonia catalyst are used to measure the apparent base-pair dissociation constants and lifetimes of Watson-Crick and mismatched base-pairs, as well as the solvent accessibility of the unpaired imino protons in the complex. The exchange characteristics of the imino protons identify the existence of four additional hydrogen bonds stabilizing the conformation of the asymmetric ATP-binding internal loop that were not detected by NOEs and coupling constants alone, but are readily accommodated in the previously reported solution structure of the AMP-RNA aptamer complex published from our laboratory. The hydrogen exchange kinetics of the non-Watson-Crick pairs in the asymmetric internal loop of the AMP-RNA aptamer complex have been characterized and yield apparent dissociation constants (alphaKd) that range from 10(-2) to 10(-7). Surprisingly, three of these alphaKd values are amongst the lowest measured for all base-pairs in the AMP-RNA aptamer complex. Comparative studies of hydrogen exchange of the imino protons in the free RNA aptamer and the AMP-RNA aptamer complex establish that complexation stabilizes not only the bases within the ATP-binding asymmetric internal loop, but also the flanking stem base-pairs (two pairs on either side) of the binding site. We also outline some preliminary results related to the exchange properties of a sugar 2'-hydroxyl proton of a guanosine residue involved in a novel hydrogen bond that has been shown to contribute to the immobilization of the bound AMP by the RNA aptamer, and whose resonance is narrow and downfield shifted in the spectrum.

The 5S rRNA loop E: chemical probing and phylogenetic data versus crystal structure.

PubMed

Leontis, N B; Westhof, E

1998-09-01

A significant fraction of the bases in a folded, structured RNA molecule participate in noncanonical base pairing interactions, often in the context of internal loops or multi-helix junction loops. The appearance of each new high-resolution RNA structure provides welcome data to guide efforts to understand and predict RNA 3D structure, especially when the RNA in question is a functionally conserved molecule. The recent publication of the crystal structure of the "Loop E" region of bacterial 5S ribosomal RNA is such an event [Correll CC, Freeborn B, Moore PB, Steitz TA, 1997, Cell 91:705-712]. In addition to providing more examples of already established noncanonical base pairs, such as purine-purine sheared pairings, trans-Hoogsteen UA, and GU wobble pairs, the structure provides the first high-resolution views of two new purine-purine pairings and a new GU pairing. The goal of the present analysis is to expand the capabilities of both chemical probing and phylogenetic analysis to predict with greater accuracy the structures of RNA molecules. First, in light of existing chemical probing data, we investigate what lessons could be learned regarding the interpretation of this widely used method of RNA structure probing. Then we analyze the 3D structure with reference to molecular phylogeny data (assuming conservation of function) to discover what alternative base pairings are geometrically compatible with the structure. The comparisons between previous modeling efforts and crystal structures show that the intricate involvements of ions and water molecules in the maintenance of non-Watson-Crick pairs render the process of correctly identifying the interacting sites in such pairs treacherous, except in cases of trans-Hoogsteen A/U or sheared A/G pairs for the adenine N1 site. The phylogenetic analysis identifies A/A, A/C, A/U and C/A, C/C, and C/U pairings isosteric with sheared A/G, as well as A/A and A/C pairings isosteric with both G/U and G/G bifurcated pairings. Thus, each non-Watson-Crick pair could be characterized by a phylogenetic signature of variations between isosteric-like pairings. In addition to the conservative changes, which form a dictionary of pairings isosterically compatible with those observed in the crystal structure, concerted changes involving several base pairs also occur. The latter covariations may indicate transitions between related but distinctive motifs within the loop E of 5S ribosomal RNA.

The electrostatic characteristics of G·U wobble base pairs

PubMed Central

Xu, Darui; Landon, Theresa; Greenbaum, Nancy L.; Fenley, Marcia O.

2007-01-01

G·U wobble base pairs are the most common and highly conserved non-Watson–Crick base pairs in RNA. Previous surface maps imply uniformly negative electrostatic potential at the major groove of G·U wobble base pairs embedded in RNA helices, suitable for entrapment of cationic ligands. In this work, we have used a Poisson–Boltzmann approach to gain a more detailed and accurate characterization of the electrostatic profile. We found that the major groove edge of an isolated G·U wobble displays distinctly enhanced negativity compared with standard GC or AU base pairs; however, in the context of different helical motifs, the electrostatic pattern varies. G·U wobbles with distinct widening have similar major groove electrostatic potentials to their canonical counterparts, whereas those with minimal widening exhibit significantly enhanced electronegativity, ranging from 0.8 to 2.5 kT/e, depending upon structural features. We propose that the negativity at the major groove of G·U wobble base pairs is determined by the combined effect of the base atoms and the sugar-phosphate backbone, which is impacted by stacking pattern and groove width as a result of base sequence. These findings are significant in that they provide predictive power with respect to which G·U sites in RNA are most likely to bind cationic ligands. PMID:17526525

A uniform database of teleseismic shear wave splitting measurements for the western and central United States

NASA Astrophysics Data System (ADS)

Liu, Kelly H.; Elsheikh, Ahmed; Lemnifi, Awad; Purevsuren, Uranbaigal; Ray, Melissa; Refayee, Hesham; Yang, Bin B.; Yu, Youqiang; Gao, Stephen S.

2014-05-01

We present a shear wave splitting (SWS) database for the western and central United States as part of a lasting effort to build a uniform SWS database for the entire North America. The SWS measurements were obtained by minimizing the energy on the transverse component of the PKS, SKKS, and SKS phases. Each of the individual measurements was visually checked to ensure quality. This version of the database contains 16,105 pairs of splitting parameters. The data used to generate the parameters were recorded by 1774 digital broadband seismic stations over the period of 1989-2012, and represented all the available data from both permanent and portable seismic networks archived at the Incorporated Research Institutions for Seismology Data Management Center in the area of 26.00°N to 50.00°N and 125.00°W to 90.00°W. About 10,000 pairs of the measurements were from the 1092 USArray Transportable Array stations. The results show that approximately 2/3 of the fast orientations are within 30° from the absolute plate motion (APM) direction of the North American plate, and most of the largest departures with the APM are located along the eastern boundary of the western US orogenic zone and in the central Great Basins. The splitting times observed in the western US are larger than, and those in the central US are comparable with the global average of 1.0 s. The uniform database has an unprecedented spatial coverage and can be used for various investigations of the structure and dynamics of the Earth.

Reactivity of cytosine and thymine in single-base-pair mismatches with hydroxylamine and osmium tetroxide and its application to the study of mutations.

PubMed Central

Cotton, R G; Rodrigues, N R; Campbell, R D

1988-01-01

The chemical reactivity of thymine (T), when mismatched with the bases cytosine, guanine, and thymine, and of cytosine (C), when mismatched with thymine, adenine, and cytosine, has been examined. Heteroduplex DNAs containing such mismatched base pairs were first incubated with osmium tetroxide (for T and C mismatches) or hydroxylamine (for C mismatches) and then incubated with piperidine to cleave the DNA at the modified mismatched base. This cleavage was studied with an internally labeled strand containing the mismatched T or C, such that DNA cleavage and thus reactivity could be detected by gel electrophoresis. Cleavage at a total of 13 T and 21 C mismatches isolated (by at least three properly paired bases on both sides) single-base-pair mismatches was identified. All T or C mismatches studied were cleaved. By using end-labeled DNA probes containing T or C single-base-pair mismatches and conditions for limited cleavage, we were able to show that cleavage was at the base predicted by sequence analysis and that mismatches in a length of DNA could be readily detected by such an approach. This procedure may enable detection of all single-base-pair mismatches by use of sense and antisense probes and thus may be used to identify the mutated base and its position in a heteroduplex. Images PMID:3260032

Disc rotors with permanent magnets for brushless DC motor

DOEpatents

Hawsey, Robert A.; Bailey, J. Milton

1992-01-01

A brushless dc permanent magnet motor drives an autonomous underwater vehe. In one embodiment, the motor comprises four substantially flat stators in stacked relationship, with pairs of the stators axially spaced, each of the stators comprising a tape-wound stator coil, and first and second substantially flat rotors disposed between the spaced pairs of stators. Each of the rotors includes an annular array of permanent magnets embedded therein. A first shaft is connected to the first rotor and a second, concentric shaft is connected to the second rotor, and a drive unit causes rotation of the two shafts in opposite directions. The second shaft comprises a hollow tube having a central bore in which the first shaft is disposed. Two different sets of bearings support the first and second shafts. In another embodiment, the motor comprises two ironless stators and pairs of rotors mounted on opposite sides of the stators and driven by counterrotating shafts.

Bipropellant propulsion with reciprocating pumps

NASA Astrophysics Data System (ADS)

Whitehead, John C.

1993-06-01

A pressure regulated gas generator rocket cycle with alternately pressurized pairs of reciprocating pumps offers thrust-on-demand operation with significantly lower inert mass than conventional spacecraft liquid propulsion systems. The operation of bipropellant feed systems with reciprocating pumps is explained, with consideration for both short and long term missions. There are several methods for startup and shutdown of this self-starting pump-fed system, with preference determined by thrust duty cycle and mission duration. Progress to date includes extensive development testing of components unique to this type of system, and several live tests with monopropellant hydrazine. Pneumatic pump control valves which render pistons and bellows automatically responsive to downstream liquid demand are significantly simpler than those described previously. A compact pumpset mounted to central liquid manifolds has a pair of oxidizer pumps pneumatically slaved to a pair of fuel pumps to reduce vibration. A warm gas pressure reducer for tank expulsion can eliminate any remaining need for inert gas storage.

A Family of Zinc Finger Proteins Is Required forChromosome-specific Pairing and Synapsis during Meiosis in C.elegans

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

Phillips, Carolyn M.; Dernburg, Abby F.

2006-06-07

Homologous chromosome pairing and synapsis are prerequisitefor accurate chromosome segregation during meiosis. Here, we show that afamily of four related C2H2 zinc-finger proteins plays a central role inthese events in C. elegans. These proteins are encoded within a tandemgene cluster. In addition to the X-specific HIM-8 protein, threeadditional paralogs collectively mediate the behavior of the fiveautosomes. Each chromosome relies on a specific member of the family topair and synapse with its homolog. These "ZIM" proteins concentrate atspecial regions called meiotic pairing centers on the correspondingchromosomes. These sites are dispersed along the nuclear envelope duringearly meiotic prophase, suggesting a role analogousmore » to thetelomere-mediated meiotic bouquet in other organisms. To gain insightinto the evolution of these components, wecharacterized homologs in C.briggsae and C. remanei, which revealed changes in copy number of thisgene family within the nematode lineage.« less

Goldstone mode and pair-breaking excitations in atomic Fermi superfluids

NASA Astrophysics Data System (ADS)

Hoinka, Sascha; Dyke, Paul; Lingham, Marcus G.; Kinnunen, Jami J.; Bruun, Georg M.; Vale, Chris J.

2017-10-01

Spontaneous symmetry breaking is a central paradigm of elementary particle physics, magnetism, superfluidity and superconductivity. According to Goldstone's theorem, phase transitions that break continuous symmetries lead to the existence of gapless excitations in the long-wavelength limit. These Goldstone modes can become the dominant low-energy excitation, showing that symmetry breaking has a profound impact on the physical properties of matter. Here, we present a comprehensive study of the elementary excitations in a homogeneous strongly interacting Fermi gas through the crossover from a Bardeen-Cooper-Schrieffer (BCS) superfluid to a Bose-Einstein condensate (BEC) of molecules using two-photon Bragg spectroscopy. The spectra exhibit a discrete Goldstone mode, associated with the broken-symmetry superfluid phase, as well as pair-breaking single-particle excitations. Our techniques yield a direct determination of the superfluid pairing gap and speed of sound in close agreement with strong-coupling theories.

Bilateral Parietal Cortex Damage Does Not Impair Associative Memory for Paired Stimuli

PubMed Central

Berryhill, Marian E.; Drowos, David B.; Olson, Ingrid R.

2010-01-01

Recent neuroimaging and neuropsychological findings indicate that the posterior parietal cortex (PPC) plays an important, albeit undefined, role in episodic memory. Here we ask whether this region is specifically involved in associative aspects of episodic memory. Experiment 1 tested whether PPC damage affects the ability to learn and retrieve novel word-pair associations. Experiment 2 tested whether PPC damage affects the retrieval of object-location associations, in a spatial fan task. In both experiments, patients showed normal levels of associative memory. These findings demonstrated that PPC damage did not prevent association memory for verbal items. Finally Experiment 3 tested whether PPC damage affects memory for non-verbal audio-visual pairs. The patients performed with normal accuracy, but with significantly reduced confidence. These findings indicate that the PPC does not have a central role in association formation per se and instead, indicate that the PPC is involved in other aspects of episodic memory. PMID:20104378

Marginal and mindful: deviants in social interactions.

PubMed

Frable, D E; Blackstone, T; Scherbaum, C

1990-07-01

Master status people's behavior, physical appearance, or life circumstance is statistically unusual and centrally defining (e.g., the physically attractive, the obese, the intellectually gifted, the facially scarred, the talented, the athletic, Blacks, gays, the wealthy, rape and incest victims). These individuals were paired with people without such conditions. Each pair was left alone on a pretext and covertly videotaped. Pairs were then separated; each member spontaneously recalled information about her partner and the experimental room and provided a record of her thoughts and feelings during the interaction. As hypothesized, all master status Ss were particularly likely to be mindful in social interactions; they recalled detailed information about the situation and often took their partner's perspective during the interaction. The positive or negative connotations of the master status conditions were irrelevant in predicting Ss cognitions (mindfulness) but were critical in determining Ss behaviors (interaction strategies).

Electrostatics Explains the Position-Dependent Effect of G⋅U Wobble Base Pairs on the Affinity of RNA Kissing Complexes.

PubMed

Abi-Ghanem, Josephine; Rabin, Clémence; Porrini, Massimiliano; Dausse, Eric; Toulmé, Jean-Jacques; Gabelica, Valérie

2017-10-06

In the RNA realm, non-Watson-Crick base pairs are abundant and can affect both the RNA 3D structure and its function. Here, we investigated the formation of RNA kissing complexes in which the loop-loop interaction is modulated by non-Watson-Crick pairs. Mass spectrometry, surface plasmon resonance, and UV-melting experiments show that the G⋅U wobble base pair favors kissing complex formation only when placed at specific positions. We tried to rationalize this effect by molecular modeling, including molecular mechanics Poisson-Boltzmann surface area (MMPBSA) thermodynamics calculations and PBSA calculations of the electrostatic potential surfaces. Modeling reveals that the G⋅U stabilization is due to a specific electrostatic environment defined by the base pairs of the entire loop-loop region. The loop is not symmetric, and therefore the identity and position of each base pair matters. Predicting and visualizing the electrostatic environment created by a given sequence can help to design specific kissing complexes with high affinity, for potential therapeutic, nanotechnology or analytical applications. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Low black carbon concentration in agricultural soils of central and northern Ethiopia.

PubMed

Yli-Halla, Markku; Rimhanen, Karoliina; Muurinen, Johanna; Kaseva, Janne; Kahiluoto, Helena

2018-08-01

Soil carbon (C) represents the largest terrestrial carbon stock and is key for soil productivity. Major fractions of soil C consist of organic C, carbonates and black C. The turnover rate of black C is lower than that of organic C, and black C abundance decreases the vulnerablility of soil C stock to decomposition under climate change. The aim of this study was to determine the distribution of soil C in different pools and impact of agricultural management on the abundance of different species. Soil C fractions were quantified in the topsoils (0-15cm) of 23 sites in the tropical highlands of Ethiopia. The sites in central Ethiopia represented paired plots of agroforestry and adjacent control plots where cereal crops were traditionally grown in clayey soils. In the sandy loam and loam soils of northern Ethiopia, the pairs represented restrained grazing with adjacent control plots with free grazing, and terracing with cereal-based cropping with adjacent control plots without terracing. Soil C contained in carbonates, organic matter and black C along with total C was determined. The total C median was 1.5% (range 0.3-3.6%). The median proportion of organic C was 85% (range 53-94%), 6% (0-41%) for carbonate C and 6% (4-21%) for black C. An increase was observed in the organic C and black C fractions attributable to agroforestry and restrained grazing. The very low concentration of the relatively stable black C fraction and the dominance of organic C in these Ethiopian soils suggest vulnerability to degradation and the necessity for cultivation practices maintaining the C stock. Copyright © 2018 Elsevier B.V. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2016-05-01

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

The cacao pathogen Moniliophthora roreri (Marasmiaceae) possesses biallelic A and B mating loci but reproduces clonally

PubMed Central

Díaz-Valderrama, J R; Aime, M C

2016-01-01

The cacao pathogen Moniliophthora roreri belongs to the mushroom-forming family Marasmiaceae, but it has never been observed to produce a fruiting body, which calls to question its capacity for sexual reproduction. In this study, we identified potential A (HD1 and HD2) and B (pheromone precursors and pheromone receptors) mating genes in M. roreri. A PCR-based method was subsequently devised to determine the mating type for a set of 47 isolates from across the geographic range of the fungus. We developed and generated an 11-marker microsatellite set and conducted association and linkage disequilibrium (standardized index of association, IAs) analyses. We also performed an ancestral reconstruction analysis to show that the ancestor of M. roreri is predicted to be heterothallic and tetrapolar, which together with sliding window analyses support that the A and B mating loci are likely unlinked and follow a tetrapolar organization within the genome. The A locus is composed of a pair of HD1 and HD2 genes, whereas the B locus consists of a paired pheromone precursor, Mr_Ph4, and receptor, STE3_Mr4. Two A and B alleles but only two mating types were identified. Association analyses divided isolates into two well-defined genetically distinct groups that correlate with their mating type; IAs values show high linkage disequilibrium as is expected in clonal reproduction. Interestingly, both mating types were found in South American isolates but only one mating type was found in Central American isolates, supporting a prior hypothesis of clonal dissemination throughout Central America after a single or very few introductions of the fungus from South America. PMID:26932308

The cacao pathogen Moniliophthora roreri (Marasmiaceae) possesses biallelic A and B mating loci but reproduces clonally.

PubMed

Díaz-Valderrama, J R; Aime, M C

2016-06-01

The cacao pathogen Moniliophthora roreri belongs to the mushroom-forming family Marasmiaceae, but it has never been observed to produce a fruiting body, which calls to question its capacity for sexual reproduction. In this study, we identified potential A (HD1 and HD2) and B (pheromone precursors and pheromone receptors) mating genes in M. roreri. A PCR-based method was subsequently devised to determine the mating type for a set of 47 isolates from across the geographic range of the fungus. We developed and generated an 11-marker microsatellite set and conducted association and linkage disequilibrium (standardized index of association, IA(s)) analyses. We also performed an ancestral reconstruction analysis to show that the ancestor of M. roreri is predicted to be heterothallic and tetrapolar, which together with sliding window analyses support that the A and B mating loci are likely unlinked and follow a tetrapolar organization within the genome. The A locus is composed of a pair of HD1 and HD2 genes, whereas the B locus consists of a paired pheromone precursor, Mr_Ph4, and receptor, STE3_Mr4. Two A and B alleles but only two mating types were identified. Association analyses divided isolates into two well-defined genetically distinct groups that correlate with their mating type; IA(s) values show high linkage disequilibrium as is expected in clonal reproduction. Interestingly, both mating types were found in South American isolates but only one mating type was found in Central American isolates, supporting a prior hypothesis of clonal dissemination throughout Central America after a single or very few introductions of the fungus from South America.

Probing the central engine and environment of AGN using ARIES 1.3-m and 3.6-m telescopes

NASA Astrophysics Data System (ADS)

Chand, Hum; Rakshit, Suvendu; Jalan, Priyanka; Ojha, Vineet; Srianand, Raghunathan; Vivek, Mariappan; Mishra, Sapna; Omar, Amitesh; Kumar, Parveen; Joshi, Ravi; Gopal-Krishna; Kumar, Rathna

2018-04-01

We discuss three long term observational programmes to probe the central engine and environment of active galactic nuclei (AGN) using the recently installed ARIES 1.3-m and 3.6-m telescopes. The first programme is on the photometric reverberation mapping of low luminosity AGN by mainly using the ARIES 1.3-m telescope. The major impact of this programme other than to estimate the black hole mass will be to extend the broad line region (BLR) radius-luminosity (RBLR-LAGN) relation to the unexplored low luminosity regime, and to constrain the AGN broad line region geometry. The second programme is to use long slit spectroscopy on the ARIES 3.6-m telescope to discover new high redshift quasar pairs with angular separation less than 1-arcmin. Here, the background QSOs sight-line will be used to probe the environment of the foreground QSOs at kpc-Mpc scales. The major impact of this programme will be on the discovery of new pairs which have been missed in the SDSS survey due to fiber collision below 1-arcmin separation, and use them to understand about any excess overdensity around the QSO, any anisotropic emission of QSOs, and/or any episodic activity of QSOs. The third programme is related to spectral variability studies of the C IV broad absorption line (BAL) QSOs, based on low resolution spectroscopy using the ARIES 3.6-m telescope. Here, those most interesting cases will be monitored, where the BAL flow emerges afresh or disappears completely in the C IV trough of BAL QSOs sample as seen in SDSS multi-epoch observations. Continuous monitoring of such a sample will be important for our understanding of the nature and origin of the flow, along with their stability and dynamical evolution.

Stellar dynamics in E+E pairs of galaxies. 1: NGC 741/742, 1587/88 and 2672/73. The data

NASA Astrophysics Data System (ADS)

Bonfanti, P.; Rampazzo, R.; Combes, F.; Prugniel, P.; Sulentic, J. W.

1995-05-01

We present a kinematic study ofthree E+E galaxy pairs, NGC, 741/642, 1587/1588 (CPG 99) and 2672/2673 (CPG 175) All three pairs show a similar morpological distortion (i.e. the off-centering of inner versus outer isphototes; Davoust & Prungniel 1988) which is ascribed to the ongoing interaction. The data was obtained at the CFHT equipped with the Herzberg Spectrograph at a resolution of 0.88 A px-1 NGC741 and 2673 show significant rotation along the apparent minor axis. Both components of CPG 99 rotate very fast (with no evidence for rotation along the mirror axis of either component). None of the galaxies show abnormally high central velocity dispersion. We report some of the first clear detections of well defined velocity dispersions curves for interacting pairs. They show a systematic decrease with distance from the center, as expected for normal ellipticals. They do not show obvious heating in the outer parts as was previously reported. NGC 741 and 2672 show, respectively, possible U and inverse U-shaped structure in their velocity profiles.

The central element of the synaptonemal complex in mice is organized as a bilayered junction structure.

PubMed

Hernández-Hernández, Abrahan; Masich, Sergej; Fukuda, Tomoyuki; Kouznetsova, Anna; Sandin, Sara; Daneholt, Bertil; Höög, Christer

2016-06-01

The synaptonemal complex transiently stabilizes pairing interactions between homologous chromosomes during meiosis. Assembly of the synaptonemal complex is mediated through integration of opposing transverse filaments into a central element, a process that is poorly understood. We have, here, analyzed the localization of the transverse filament protein SYCP1 and the central element proteins SYCE1, SYCE2 and SYCE3 within the central region of the synaptonemal complex in mouse spermatocytes using immunoelectron microscopy. Distribution of immuno-gold particles in a lateral view of the synaptonemal complex, supported by protein interaction data, suggest that the N-terminal region of SYCP1 and SYCE3 form a joint bilayered central structure, and that SYCE1 and SYCE2 localize in between the two layers. We find that disruption of SYCE2 and TEX12 (a fourth central element protein) localization to the central element abolishes central alignment of the N-terminal region of SYCP1. Thus, our results show that all four central element proteins, in an interdependent manner, contribute to stabilization of opposing N-terminal regions of SYCP1, forming a bilayered transverse-filament-central-element junction structure that promotes synaptonemal complex formation and synapsis. © 2016. Published by The Company of Biologists Ltd.

The Impact of a Peer-Learning Agent Based on Pair Programming in a Programming Course

ERIC Educational Resources Information Center

Han, Keun-Woo; Lee, EunKyoung; Lee, YoungJun

2010-01-01

This paper analyzes the educational effects of a peer-learning agent based on pair programming in programming courses. A peer-learning agent system was developed to facilitate the learning of a programming language through the use of pair programming strategies. This system is based on the role of a peer-learning agent from pedagogical and…

Weak nanoscale chaos and anomalous relaxation in DNA

NASA Astrophysics Data System (ADS)

Mazur, Alexey K.

2017-06-01

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

Distribution of Base Pair Alternations in a Periodic DNA Chain: Application of Pólya Counting to a Physical System

NASA Astrophysics Data System (ADS)

Hillebrand, Malcolm; Paterson-Jones, Guy; Kalosakas, George; Skokos, Charalampos

2018-03-01

In modeling DNA chains, the number of alternations between Adenine-Thymine (AT) and Guanine-Cytosine (GC) base pairs can be considered as a measure of the heterogeneity of the chain, which in turn could affect its dynamics. A probability distribution function of the number of these alternations is derived for circular or periodic DNA. Since there are several symmetries to account for in the periodic chain, necklace counting methods are used. In particular, Polya's Enumeration Theorem is extended for the case of a group action that preserves partitioned necklaces. This, along with the treatment of generating functions as formal power series, allows for the direct calculation of the number of possible necklaces with a given number of AT base pairs, GC base pairs and alternations. The theoretically obtained probability distribution functions of the number of alternations are accurately reproduced by Monte Carlo simulations and fitted by Gaussians. The effect of the number of base pairs on the characteristics of these distributions is also discussed, as well as the effect of the ratios of the numbers of AT and GC base pairs.

Weak nanoscale chaos and anomalous relaxation in DNA.

PubMed

Mazur, Alexey K

2017-06-01

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

Seismic imaging of the southern California plate-boundary around the South-Central Transverse Ranges using double-difference tomography

NASA Astrophysics Data System (ADS)

Share, P. E.; Ben-Zion, Y.; Thurber, C. H.; Zhang, H.; Guo, H.

2017-12-01

We derive P and S seismic velocities within and around the South-Central Transverse Ranges section of the San Andreas Fault (SAF), using a new double-difference tomography algorithm incorporating both event-pair and station-pair differential times. The event-pair data can determine high-resolution relative earthquake locations and resolve fine-scale structure in seismogenic zones, whereas station-pair data allow for better absolute locations and higher resolution of structure near the surface where stations are most dense. The tomographic results are based on arrival times of P and S waves generated by 17,753 M>1 local events from 1/1/2010 to 6/30/2015 recorded by 259 stations within a 222 km x 164 km region. The resulting P and S velocity models include low velocities along major fault segments and across-fault velocity contrasts. For example, at depths <7 km, low velocity anomalies delineate the SAF from Cajon Pass to Coachella Valley, with the exception around San Gorgonio Pass (SGP) where a relatively fast rock body cuts across the fault. Extensive faulting and Pelona schist manifest as low velocities throughout the San Bernardino Basin (SBB). High velocity granites abut the SBB to the SW and NE, forming prominent velocity contrasts across the northern San Jacinto Fault Zone (SJFZ) and the SAF, respectively. At depths of 9-11 km, the models also show a velocity contrast with an areal extent of >50 km parallel to the SAF around Coachella Valley but offset to the NE by 13 km. This is interpreted to mark a dipping section of the SAF that separates granites at depth in the SW from gneisses and schists in the NE. Analysis of fault zone head waves propagating along these sections of the SAF and SJFZ show that major bimaterial interfaces are associated with the observed velocity contrasts. Additional features within the models include elongated low velocity anomalies extending from the SJFZ trifurcation area, which itself has associated low velocity at great depth (>14 km), to the Elsinore Fault in the SW. Moreover, a deep (>13 km) velocity contrast appears beneath the SBB with an east-west strike oblique to both the northern SJFZ and SAF traces. The latter is potentially related to the ancestral Banning Fault, which dips to the north, separating low velocity Pelona schist in the north from high velocity granites in the south.

Differential stabilities and sequence-dependent base pair opening dynamics of Watson-Crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine.

PubMed

Szulik, Marta W; Pallan, Pradeep S; Nocek, Boguslaw; Voehler, Markus; Banerjee, Surajit; Brooks, Sonja; Joachimiak, Andrzej; Egli, Martin; Eichman, Brandt F; Stone, Michael P

2015-02-10

5-Hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) form during active demethylation of 5-methylcytosine (5mC) and are implicated in epigenetic regulation of the genome. They are differentially processed by thymine DNA glycosylase (TDG), an enzyme involved in active demethylation of 5mC. Three modified Dickerson-Drew dodecamer (DDD) sequences, amenable to crystallographic and spectroscopic analyses and containing the 5'-CG-3' sequence associated with genomic cytosine methylation, containing 5hmC, 5fC, or 5caC placed site-specifically into the 5'-T(8)X(9)G(10)-3' sequence of the DDD, were compared. The presence of 5caC at the X(9) base increased the stability of the DDD, whereas 5hmC or 5fC did not. Both 5hmC and 5fC increased imino proton exchange rates and calculated rate constants for base pair opening at the neighboring base pair A(5):T(8), whereas 5caC did not. At the oxidized base pair G(4):X(9), 5fC exhibited an increase in the imino proton exchange rate and the calculated kop. In all cases, minimal effects to imino proton exchange rates occurred at the neighboring base pair C(3):G(10). No evidence was observed for imino tautomerization, accompanied by wobble base pairing, for 5hmC, 5fC, or 5caC when positioned at base pair G(4):X(9); each favored Watson-Crick base pairing. However, both 5fC and 5caC exhibited intranucleobase hydrogen bonding between their formyl or carboxyl oxygens, respectively, and the adjacent cytosine N(4) exocyclic amines. The lesion-specific differences observed in the DDD may be implicated in recognition of 5hmC, 5fC, or 5caC in DNA by TDG. However, they do not correlate with differential excision of 5hmC, 5fC, or 5caC by TDG, which may be mediated by differences in transition states of the enzyme-bound complexes.

Differential stabilities and sequence-dependent base pair opening dynamics of Watson–Crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine

DOE PAGES

Szulik, Marta W.; Pallan, Pradeep S.; Nocek, Boguslaw; ...

2015-01-29

5-Hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) form during active demethylation of 5-methylcytosine (5mC) and are implicated in epigenetic regulation of the genome. They are differentially processed by thymine DNA glycosylase (TDG), an enzyme involved in active demethylation of 5mC. Three modified Dickerson–Drew dodecamer (DDD) sequences, amenable to crystallographic and spectroscopic analyses and containing the 5'-CG-3' sequence associated with genomic cytosine methylation, containing 5hmC, 5fC, or 5caC placed site-specifically into the 5'-T 8X 9G 10-3' sequence of the DDD, were compared. The presence of 5caC at the X9 base increased the stability of the DDD, whereas 5hmC or 5fC didmore » not. Both 5hmC and 5fC increased imino proton exchange rates and calculated rate constants for base pair opening at the neighboring base pair A 5:T 8, whereas 5caC did not. At the oxidized base pair G 4:X 9, 5fC exhibited an increase in the imino proton exchange rate and the calculated k op. In all cases, minimal effects to imino proton exchange rates occurred at the neighboring base pair C 3:G 10. No evidence was observed for imino tautomerization, accompanied by wobble base pairing, for 5hmC, 5fC, or 5caC when positioned at base pair G 4:X 9; each favored Watson–Crick base pairing. However, both 5fC and 5caC exhibited intranucleobase hydrogen bonding between their formyl or carboxyl oxygens, respectively, and the adjacent cytosine N 4 exocyclic amines. The lesion-specific differences observed in the DDD may be implicated in recognition of 5hmC, 5fC, or 5caC in DNA by TDG. Furthermore, they do not correlate with differential excision of 5hmC, 5fC, or 5caC by TDG, which may be mediated by differences in transition states of the enzyme-bound complexes.« less

Differential Stabilities and Sequence-Dependent Base Pair Opening Dynamics of Watson–Crick Base Pairs with 5-Hydroxymethylcytosine, 5-Formylcytosine, or 5-Carboxylcytosine

PubMed Central

2016-01-01

5-Hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) form during active demethylation of 5-methylcytosine (5mC) and are implicated in epigenetic regulation of the genome. They are differentially processed by thymine DNA glycosylase (TDG), an enzyme involved in active demethylation of 5mC. Three modified Dickerson–Drew dodecamer (DDD) sequences, amenable to crystallographic and spectroscopic analyses and containing the 5′-CG-3′ sequence associated with genomic cytosine methylation, containing 5hmC, 5fC, or 5caC placed site-specifically into the 5′-T8X9G10-3′ sequence of the DDD, were compared. The presence of 5caC at the X9 base increased the stability of the DDD, whereas 5hmC or 5fC did not. Both 5hmC and 5fC increased imino proton exchange rates and calculated rate constants for base pair opening at the neighboring base pair A5:T8, whereas 5caC did not. At the oxidized base pair G4:X9, 5fC exhibited an increase in the imino proton exchange rate and the calculated kop. In all cases, minimal effects to imino proton exchange rates occurred at the neighboring base pair C3:G10. No evidence was observed for imino tautomerization, accompanied by wobble base pairing, for 5hmC, 5fC, or 5caC when positioned at base pair G4:X9; each favored Watson–Crick base pairing. However, both 5fC and 5caC exhibited intranucleobase hydrogen bonding between their formyl or carboxyl oxygens, respectively, and the adjacent cytosine N4 exocyclic amines. The lesion-specific differences observed in the DDD may be implicated in recognition of 5hmC, 5fC, or 5caC in DNA by TDG. However, they do not correlate with differential excision of 5hmC, 5fC, or 5caC by TDG, which may be mediated by differences in transition states of the enzyme-bound complexes. PMID:25632825

Layer-Based Approach for Image Pair Fusion.

PubMed

Son, Chang-Hwan; Zhang, Xiao-Ping

2016-04-20

Recently, image pairs, such as noisy and blurred images or infrared and noisy images, have been considered as a solution to provide high-quality photographs under low lighting conditions. In this paper, a new method for decomposing the image pairs into two layers, i.e., the base layer and the detail layer, is proposed for image pair fusion. In the case of infrared and noisy images, simple naive fusion leads to unsatisfactory results due to the discrepancies in brightness and image structures between the image pair. To address this problem, a local contrast-preserving conversion method is first proposed to create a new base layer of the infrared image, which can have visual appearance similar to another base layer such as the denoised noisy image. Then, a new way of designing three types of detail layers from the given noisy and infrared images is presented. To estimate the noise-free and unknown detail layer from the three designed detail layers, the optimization framework is modeled with residual-based sparsity and patch redundancy priors. To better suppress the noise, an iterative approach that updates the detail layer of the noisy image is adopted via a feedback loop. This proposed layer-based method can also be applied to fuse another noisy and blurred image pair. The experimental results show that the proposed method is effective for solving the image pair fusion problem.

Base pairing among three cis-acting sequences contributes to template switching during hepadnavirus reverse transcription

PubMed Central

Liu, Ning; Tian, Ru; Loeb, Daniel D.

2003-01-01

Synthesis of the relaxed-circular (RC) DNA genome of hepadnaviruses requires two template switches during plus-strand DNA synthesis: primer translocation and circularization. Although primer translocation and circularization use different donor and acceptor sequences, and are distinct temporally, they share the common theme of switching from one end of the minus-strand template to the other end. Studies of duck hepatitis B virus have indicated that, in addition to the donor and acceptor sequences, three other cis-acting sequences, named 3E, M, and 5E, are required for the synthesis of RC DNA by contributing to primer translocation and circularization. The mechanism by which 3E, M, and 5E act was not known. We present evidence that these sequences function by base pairing with each other within the minus-strand template. 3E base-pairs with one portion of M (M3) and 5E base-pairs with an adjacent portion of M (M5). We found that disrupting base pairing between 3E and M3 and between 5E and M5 inhibited primer translocation and circularization. More importantly, restoring base pairing with mutant sequences restored the production of RC DNA. These results are consistent with the model that, within duck hepatitis B virus capsids, the ends of the minus-strand template are juxtaposed via base pairing to facilitate the two template switches during plus-strand DNA synthesis. PMID:12578983

DNA polymerase catalysis in the absence of Watson-Crick hydrogen bonds

PubMed Central

Potapova, Olga; Chan, Chikio; DeLucia, Angela M.; Helquist, Sandra A.; Kool, Eric T.; Grindley, Nigel D. F.; Joyce, Catherine M.

2008-01-01

We report the first pre-steady-state kinetic studies of DNA replication in the absence of hydrogen bonds. We have used nonpolar nucleotide analogues that mimic the shape of a Watson-Crick base pair in order to investigate the kinetic consequences of a lack of hydrogen bonds in the polymerase reaction catalyzed by the Klenow fragment of DNA Polymerase I from Escherichia coli. With a thymine isostere lacking hydrogen bonding ability in the nascent pair, the efficiency (kpol/Kd) of the polymerase reaction is decreased by 30-fold, affecting ground state (Kd) and transition state (kpol) approximately equally. When both thymine and adenine analogues in the nascent pair lack hydrogen bonding ability, the efficiency of the polymerase reaction is decreased by about 1000-fold, with most the decrease attributable to the transition state. Reactions using nonpolar analogues at the primer terminal base pair demonstrated the requirement for a hydrogen bond between the polymerase and the minor groove of the primer-terminal base. The R668A mutation of Klenow fragment abolished this requirement, identifying R668 as the probable hydrogen bond donor. Detailed examination of the kinetic data suggested that Klenow fragment has an extremely low tolerance of even minor deviations of the analogue base pairs from ideal Watson-Crick geometry. Consistent with this idea, some analogue pairings were better tolerated by Klenow fragment mutants having more spacious active sites. By contrast, the Y-family polymerase Dbh was much less sensitive to changes in base pair dimensions, and more dependent on hydrogen bonding between base-paired partners. PMID:16411765

76 FR 72713 - Government-Owned Inventions; Availability for Licensing

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-25

... pitfall to avermectins is central nervous system (CNS) toxicities in herding dogs. As a result, all new... containing the canine wild-type gene (Yancy 2 line). The paired mouse system can be utilized to assess the... xerostomia (dry mouth) that is caused by immune system attack on moisture producing salivary glands...

Who Needs Lewis Structures to Get VSEPR Geometries?

ERIC Educational Resources Information Center

Lindmark, Alan F.

2010-01-01

Teaching the VSEPR (valence shell electron-pair repulsion) model can be a tedious process. Traditionally, Lewis structures are drawn and the number of "electron clouds" (groups) around the central atom are counted and related to the standard VSEPR table of possible geometries. A simpler method to deduce the VSEPR structure without first drawing…

47 CFR Appendix to Part 36 - Glossary

Code of Federal Regulations, 2010 CFR

2010-10-01

... such terms in the separation procedures. Terms which are defined in the text of this part are not.... Complement (of cable) A group of conductors of the same general type (e.g., quadded, paired) within a single... unit which is normally dependent upon the central processor of the host office for call processing...

High-quality genome of the peach scab pathogen, Venturia carpophila

USDA-ARS?s Scientific Manuscript database

Venturia carpophila causes peach scab, a disease that renders peach (Prunus persica) fruit unmarketable. We report a high-quality draft genome (36.9 Mb) of V. carpophila from an isolate collected from a peach tree in central Georgia. The genome was sequenced by MiSeq using an Illumina paired-end lib...

Sound Change and Mobility in Los Angeles

ERIC Educational Resources Information Center

Johnson, Lawrence

1975-01-01

Deals with the shift of the low-back vowel as in 'caught' to a low-central vowel as in 'cot' thereby merging such pairs as caught/cot, dawn/Don, and stalk/stock. The causes and the sociolinguistic implications of this shift are discussed. The majority of the informants were from West Los Angeles. (TL)

Evidence for Structural Alignment during Similarity Judgments.

ERIC Educational Resources Information Center

Markman, Arthur B.; Gentner, Dedre

Similarity plays a central role in cognitive theories. Research has demonstrated that the similarity of a pair increases with its commonalities and decreases with its differences. These common and distinctive elements can take the form of parts of objects, relations between parts of properties of whole objects. Previous work has been unable to…

Movement and spatial proximity patterns of rangeland-raised Raramuri Criollo cow-calf pairs

USDA-ARS?s Scientific Manuscript database

The objective of this study was to compare movement patterns of nursing vs. nonnursing mature cows and to characterize cow-calf proximity patterns in two herds of Raramuri Criollo cattle. Herds grazed rangeland pastures in southern New Mexico (4355 ha) and west-central Chihuahua, Mexico (633 ha)'' A...

Ranking fluctuating asymmetry in a dot figure and the significant impact of imagining a face.

PubMed

Neby, Magne; Ivar, Folstad

2013-01-01

Fluctuating asymmetry and averageness is correlated with our perception of beauty in human faces. Yet, whether deviations of centrality in the positioning of the eyes, the nose, and the mouth have different effects on our perception of asymmetry in a holistic human face, is still uncertain. In this study we aimed to test the relative effect of decentralising the horizontal position of three sets of paired dots representing eyes, nostrils, or mouth from the vertical midline of ambiguous dot figures, vaguely resembling a face. The figures were ranked according to perceived asymmetry by human observers. When associating the figures with non-facial objects (eg a butterfly), none of the figures' rank distribution differed from each other. However, when observers imagined the figures to represent a human face, the figure with the decentralised pair of dots representing the nostrils was significantly ranked as more asymmetric than the other figures. This result provides indications that the brain may deal with information about facial asymmetry and averageness heavily depending on the centrality of the nasal region.

Bending patterns of chlamydomonas flagella: III. A radial spoke head deficient mutant and a central pair deficient mutant.

PubMed

Brokaw, C J; Luck, D J

1985-01-01

Flash photomicrography at frequencies up to 300 Hz and computer-assisted image analysis have been used to obtain parameters describing the flagellar bending patterns of mutants of Chlamydomonas reinhardtii. All strains contained the uni1 mutation, to facilitate photography. The radial spoke head deficient mutant pf17, and the central pair deficient mutant, pf15, in combination with suppressor mutations that restore motility without restoring the ultrastructural or biochemical deficiencies, both generate forward mode bending patterns with increased shear amplitude and decreased asymmetry relative to the "wild-type" uni1 flagella described previously. In the reverse beating mode, the suppressed pf17 mutants generate reverse bending patterns with large shear amplitudes. Reverse beating of the suppressed pf15 mutants is rare. There is a reciprocal relationship between increased shear amplitude and decreased beat frequency, so that the velocity of sliding between flagellar microtubules is not increased by an increase in shear amplitude. The suppressor mutations alone cause decreased frequency and sliding velocity in both forward and reverse mode beating, with little change in shear amplitude or symmetry.

Nonlinear Stability and Structure of Compressible Reacting Mixing Layers

NASA Technical Reports Server (NTRS)

Day, M. J.; Mansour, N. N.; Reynolds, W. C.

2000-01-01

The parabolized stability equations (PSE) are used to investigate issues of nonlinear flow development and mixing in compressible reacting shear layers. Particular interest is placed on investigating the change in flow structure that occurs when compressibility and heat release are added to the flow. These conditions allow the 'outer' instability modes- one associated with each of the fast and slow streams-to dominate over the 'central', Kelvin-Helmholtz mode that unaccompanied in incompressible nonreacting mixing layers. Analysis of scalar probability density functions in flows with dominant outer modes demonstrates the ineffective, one-sided nature of mixing that accompany these flow structures. Colayer conditions, where two modes have equal growth rate and the mixing layer is formed by two sets of vortices, offer some opportunity for mixing enhancement. Their extent, however, is found to be limited in the mixing layer's parameter space. Extensive validation of the PSE technique also provides a unique perspective on central- mode vortex pairing, further supporting the view that pairing is primarily governed perspective sheds insight on how linear stability theory is able to provide such an accurate prediction of experimentally-observed, fully nonlinear flow phenomenon.

Base drive circuit

DOEpatents

Lange, A.C.

1995-04-04

An improved base drive circuit having a level shifter for providing bistable input signals to a pair of non-linear delays. The non-linear delays provide gate control to a corresponding pair of field effect transistors through a corresponding pair of buffer components. The non-linear delays provide delayed turn-on for each of the field effect transistors while an associated pair of transistors shunt the non-linear delays during turn-off of the associated field effect transistor. 2 figures.

An Intelligent Model for Pairs Trading Using Genetic Algorithms.

PubMed

Huang, Chien-Feng; Hsu, Chi-Jen; Chen, Chi-Chung; Chang, Bao Rong; Li, Chen-An

2015-01-01

Pairs trading is an important and challenging research area in computational finance, in which pairs of stocks are bought and sold in pair combinations for arbitrage opportunities. Traditional methods that solve this set of problems mostly rely on statistical methods such as regression. In contrast to the statistical approaches, recent advances in computational intelligence (CI) are leading to promising opportunities for solving problems in the financial applications more effectively. In this paper, we present a novel methodology for pairs trading using genetic algorithms (GA). Our results showed that the GA-based models are able to significantly outperform the benchmark and our proposed method is capable of generating robust models to tackle the dynamic characteristics in the financial application studied. Based upon the promising results obtained, we expect this GA-based method to advance the research in computational intelligence for finance and provide an effective solution to pairs trading for investment in practice.

An Intelligent Model for Pairs Trading Using Genetic Algorithms

PubMed Central

Hsu, Chi-Jen; Chen, Chi-Chung; Li, Chen-An

2015-01-01

Pairs trading is an important and challenging research area in computational finance, in which pairs of stocks are bought and sold in pair combinations for arbitrage opportunities. Traditional methods that solve this set of problems mostly rely on statistical methods such as regression. In contrast to the statistical approaches, recent advances in computational intelligence (CI) are leading to promising opportunities for solving problems in the financial applications more effectively. In this paper, we present a novel methodology for pairs trading using genetic algorithms (GA). Our results showed that the GA-based models are able to significantly outperform the benchmark and our proposed method is capable of generating robust models to tackle the dynamic characteristics in the financial application studied. Based upon the promising results obtained, we expect this GA-based method to advance the research in computational intelligence for finance and provide an effective solution to pairs trading for investment in practice. PMID:26339236

Multi-Instrument Analysis of a Traveling Convection Vortex Event on July 24, 1996 Coordinated with the Polar UVI

NASA Technical Reports Server (NTRS)

Sitar, R. J.; Clauer, C. R.; Baker, J. B.; Ridley, A. J.; Cumnock, J.; Germany, G. A.; Spann, J. F., Jr.; Brittnacher, M. J.; Parks, G. K.

1998-01-01

We present the analysis of a coordinated set of observations from the POLAR Ultraviolet Imager (UVI), ground magnetometers, incoherent scatter radar, solar wind monitors, DMSP and GOES satellites, focused on a traveling convection vortex (TCV) event on 24th July 1996. Starting at approximately 10:48 UT, around magnetometers in Greenland and northern Canada observe pulsations consistent with the passing overhead of a series of alternating TCV filed-aligned current pairs. Azimuthal scans by the Sondrestrom incoherent scatter radar located near Kangerlussuaq (formerly Sondrestrom), Greenland, at this time show strong modulation in the strength and direction of ionospheric plasma flow. The magnetometer pulsations grow in magnitude over the next hour, peaking in intensity at 11:39 UT, at which time images form the UVI instrument show a localized intensification of auroral emissions over central and western Greenland. Subsequent images show the intensification grow in strength and propagate westward (tailward) until approximately 11:58 UT at which time the intensification fades. These observations are consistent with the westward passage of two pairs of moderately intense TCVs over central Greenland followed by a third very intense TCV pair. The intensification of auroral emissions at 11:39 UT is associated with the trailing vortex of the third TCV pair, thought to be the result of an upward field aligned current. The modulated flow observed by the radar is the result of the strong electric fields associated with the impulsive TCV related field aligned current systems as they pass through the field of view of the radar. Measurements of the solar wind from the V;IND and IMP-8 spacecraft suggest that a pressure change may be responsible for triggering the first two pairs of TCVS, and that a subsequent sudden change in the orientation of the interplanetary magnetic field may have produced the intensification of the third TCV pair and the associated auroral brightening. Magnetometer data from the GOES satellite located over the eastern United States at geostationary orbit is consistent with a series of field-aligned moving tailward past the satellite. DMSP particle data indicated that the TCVs occur on field lines which map to the boundary plasma sheet (BPS).

A scaling relation between merger rate of galaxies and their close pair count

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

Jiang, C. Y.; Jing, Y. P.; Han, Jiaxin, E-mail: ypjing@sjtu.edu.cn

We study how to measure the galaxy merger rate from the observed close pair count. Using a high-resolution N-body/SPH cosmological simulation, we find an accurate scaling relation between galaxy pair counts and merger rates down to a stellar mass ratio of about 1:30. The relation explicitly accounts for the dependence on redshift (or time), on pair separation, and on mass of the two galaxies in a pair. With this relation, one can easily obtain the mean merger timescale for a close pair of galaxies. The use of virial masses, instead of the stellar mass, is motivated by the fact thatmore » the dynamical friction timescale is mainly determined by the dark matter surrounding central and satellite galaxies. This fact can also minimize the error induced by uncertainties in modeling star formation in the simulation. Since the virial mass can be determined from the well-established relation between the virial masses and the stellar masses in observations, our scaling relation can easily be applied to observations to obtain the merger rate and merger timescale. For major merger pairs (1:1-1:4) of galaxies above a stellar mass of 4 × 10{sup 10} h {sup –1} M{sub ☉} at z = 0.1, it takes about 0.31 Gyr to merge for pairs within a projected distance of 20 h {sup –1} kpc with a stellar mass ratio of 1:1, while the time goes up to 1.6 Gyr for mergers with stellar mass ratio of 1:4. Our results indicate that a single timescale usually used in the literature is not accurate to describe mergers with a stellar mass ratio spanning even a narrow range from 1:1 to 1:4.« less

Variation in the oxytocin receptor gene (OXTR) is associated with pair-bonding and social behavior

PubMed Central

Walum, Hasse; Lichtenstein, Paul; Neiderhiser, Jenae M.; Reiss, David; Ganiban, Jody M.; Spotts, Erica L.; Pedersen, Nancy L.; Anckarsäter, Henrik; Larsson, Henrik; Westberg, Lars

2011-01-01

Background In specific vole and primate species the neuropeptide Oxytocin (OT) plays a central role in the regulation of pair-bonding behavior. Here we investigate to what extent genetic variants in the oxytocin receptor gene (OXTR) are associated with pair-bonding and related social behaviors in humans. Methods We first genotyped twelve Single Nucleotide Polymorphisms (SNPs) in the Twin and Offspring Study in Sweden (TOSS, N=2309) and the Swedish Twin Study of CHild and Adolescent Development (TCHAD, N=1240) comprising measures of self-reported pair-bonding behavior. In the TOSS-sample we further investigated one the SNPs for measures of marital status and quality. Moreover, in the TCHAD sample we explored the longitudinal relationship between precursors of pair-bonding during childhood and subsequent behavior in romantic relationships. Finally, in TCHAD and in the Child and Adolescent Twin Study of Sweden (CATSS, N=1771) the association between the same SNP and childhood behaviors was investigated. Results One SNP (rs7632287) in OXTR was associated with traits reflecting pair-bonding in women in the TOSS and TCHAD samples. In girls the rs7632287 SNP was further associated with childhood social problems, which longitudinally predicted pair-bonding behavior in the TCHAD-sample. This association was replicated in the CATSS-sample in which an association between the same SNP and social interaction deficit symptoms from the autism spectrum was detected. Conclusion These results suggest an association between variation in OXTR and human pair-bonding and other social behaviors, possibly indicating that the well described influence of OT on affiliative behavior in voles could also be of importance for humans. PMID:22015110

The fidelity of replication of the three-base-pair set adenine/thymine, hypoxanthine/cytosine and 6-thiopurine/5-methyl-2-pyrimidinone with T7 DNA polymerase

PubMed Central

2004-01-01

With the goal of constructing a genetic alphabet consisting of a set of three base pairs, the fidelity of replication of the three base pairs TH (5-methyl-2-pyrimidinone)/HS (6-thiopurine; thiohypoxanthine), C/H (hypoxanthine) and T/A was evaluated using T7 DNA polymerase, a polymerase with a strong 3′→5′ exonuclease activity. An evaluation of the suitability of a new base pair for replication should include both the contribution of the fidelity of a polymerase activity and the contribution of proofreading by a 3′→5′ exonuclease activity. Using a steady-state kinetics method that included the contribution of the 3′→5′ exonuclease activity, the fidelity of replication was determined. The method determined the ratio of the apparent rate constant for the addition of a deoxynucleotide to the primer across from a template base by the polymerase activity and the rate constant for removal of the added deoxynucleotide from the primer by the 3′→5′ exonuclease activity. This ratio was designated the eni (efficiency of net incorporation). The eni of the base pair C/H was equal to or greater than the eni of T/A. The eni of the base pair TH/HS was 0.1 times that of A/T for TH in the template and 0.01 times that of A/T for HS in the template. The ratio of the eni of a mismatched deoxynucleotide to the eni of a matched deoxynucleotide was a measure of the error frequency. The error frequencies were as follows: thymine or TH opposite a template hypoxanthine, 2×10−6; HS opposite a template cytosine, <3×10−4. The remaining 24 mismatched combinations of bases gave no detectable net incorporation. Two mismatches, hypoxanthine opposite a template thymine or a template TH, showed trace incorporation in the presence of a standard dNTP complementary to the next template base. T7 DNA polymerase extended the primer beyond each of the matched base pairs of the set. The level of fidelity of replication of the three base pairs with T7 DNA polymerase suggests that they are adequate for a three-base-pair alphabet for DNA replication. PMID:15078225

The involvement of central attention in visual search is determined by task demands.

PubMed

Han, Suk Won

2017-04-01

Attention, the mechanism by which a subset of sensory inputs is prioritized over others, operates at multiple processing stages. Specifically, attention enhances weak sensory signal at the perceptual stage, while it serves to select appropriate responses or consolidate sensory representations into short-term memory at the central stage. This study investigated the independence and interaction between perceptual and central attention. To do so, I used a dual-task paradigm, pairing a four-alternative choice task with a visual search task. The results showed that central attention for response selection was engaged in perceptual processing for visual search when the number of search items increased, thereby increasing the demand for serial allocation of focal attention. By contrast, central attention and perceptual attention remained independent as far as the demand for serial shifting of focal attention remained constant; decreasing stimulus contrast or increasing the set size of a parallel search did not evoke the involvement of central attention in visual search. These results suggest that the nature of concurrent visual search process plays a crucial role in the functional interaction between two different types of attention.

Pairing States of Spin-3/2 Fermions: Symmetry-Enforced Topological Gap Functions

NASA Astrophysics Data System (ADS)

Venderbos, Jörn W. F.; Savary, Lucile; Ruhman, Jonathan; Lee, Patrick A.; Fu, Liang

2018-01-01

We study the topological properties of superconductors with paired j =3/2 quasiparticles. Higher spin Fermi surfaces can arise, for instance, in strongly spin-orbit coupled band-inverted semimetals. Examples include the Bi-based half-Heusler materials, which have recently been established as low-temperature and low-carrier density superconductors. Motivated by this experimental observation, we obtain a comprehensive symmetry-based classification of topological pairing states in systems with higher angular momentum Cooper pairing. Our study consists of two main parts. First, we develop the phenomenological theory of multicomponent (i.e., higher angular momentum) pairing by classifying the stationary points of the free energy within a Ginzburg-Landau framework. Based on the symmetry classification of stationary pairing states, we then derive the symmetry-imposed constraints on their gap structures. We find that, depending on the symmetry quantum numbers of the Cooper pairs, different types of topological pairing states can occur: fully gapped topological superconductors in class DIII, Dirac superconductors, and superconductors hosting Majorana fermions. Notably, we find a series of nematic fully gapped topological superconductors, as well as double- and triple-Dirac superconductors, with quadratic and cubic dispersion, respectively. Our approach, applied here to the case of j =3/2 Cooper pairing, is rooted in the symmetry properties of pairing states, and can therefore also be applied to other systems with higher angular momentum and high-spin pairing. We conclude by relating our results to experimentally accessible signatures in thermodynamic and dynamic probes.

Interferometry correlations in central p+Pb collisions

NASA Astrophysics Data System (ADS)

Bożek, Piotr; Bysiak, Sebastian

2018-01-01

We present results on interferometry correlations for pions emitted in central p+Pb collisions at √{s_{NN}}=5.02 TeV in a 3+1-dimensional viscous hydrodynamic model with initial conditions from the Glauber Monte Carlo model. The correlation function is calculated as a function of the pion pair rapidity. The extracted interferometry radii show a weak rapidity dependence, reflecting the lack of boost invariance of the pion distribution. A cross term between the out and long directions is found to be nonzero. The results obtained in the hydrodynamic model are in fair agreement with recent data of the ATLAS Collaboration.

Elliptic flow of electrons from beauty-hadron decays extracted from Pb-Pb collision data at √{s_NN} = 2.76 TeV

NASA Astrophysics Data System (ADS)

Moreira de Godoy, D.; Herrmann, F.; Klasen, M.; Klein-Bösing, C.; Suaide, A. A. P.

2018-05-01

We present a calculation of the elliptic flow of electrons from beauty-hadron decays in semi-central Pb-Pb collisions at centre-of-mass energy per colliding nucleon pair, represented as √{s_NN}, of 2.76 TeV. The result is obtained by the subtraction of the charm-quark contribution in the elliptic flow of electrons from heavy-flavour hadron decays in semi-central Pb-Pb collisions at √{s_NN} = 2.76 TeV recently made publicly available by the ALICE collaboration.

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

NASA Technical Reports Server (NTRS)

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

2011-01-01

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

N-H Stretching Excitations in Adenosine-Thymidine Base Pairs in Solution: Base Pair Geometries, Infrared Line Shapes and Ultrafast Vibrational Dynamics

PubMed Central

Greve, Christian; Preketes, Nicholas K.; Fidder, Henk; Costard, Rene; Koeppe, Benjamin; Heisler, Ismael A.; Mukamel, Shaul; Temps, Friedrich; Nibbering, Erik T. J.; Elsaesser, Thomas

2013-01-01

We explore the N-H stretching vibrations of adenosine-thymidine base pairs in chloroform solution with linear and nonlinear infrared spectroscopy. Based on estimates from NMR measurements and ab initio calculations, we conclude that adenosine and thymidine form hydrogen bonded base pairs in Watson-Crick, reverse Watson-Crick, Hoogsteen and reverse Hoogsteen configurations with similar probability. Steady-state concentration- and temperature dependent linear FT-IR studies, including H/D exchange experiments, reveal that these hydrogen-bonded base pairs have complex N-H/N-D stretching spectra with a multitude of spectral components. Nonlinear 2D-IR spectroscopic results, together with IR-pump-IR-probe measurements, as also corroborated by ab initio calculations, reveal that the number of N-H stretching transitions is larger than the total number of N-H stretching modes. This is explained by couplings to other modes, such as an underdamped low-frequency hydrogen-bond mode, and a Fermi resonance with NH2 bending overtone levels of the adenosine amino-group. Our results demonstrate that modeling based on local N-H stretching vibrations only is not sufficient and call for further refinement of the description of the N-H stretching manifolds of nucleic acid base pairs of adenosine and thymidine, incorporating a multitude of couplings with fingerprint and low-frequency modes. PMID:23234439

Identification and Interpretation of a Surge-type Glacier in the Central Tibetan Plateau with Multi-source Satellite InSAR Datasets

NASA Astrophysics Data System (ADS)

Liu, L.; Jiang, L.; Sun, Y.; Wang, H.

2014-12-01

Surge-type glaciers are very important to understanding of glacier dynamics and mass balance. They generally experience well-defined cyclical non-steady flow, with alternation between short active phases (months to years) and a longer quiescent phase (years to decades). Previous studies reported that most of surge-type glaciers in the High Asian Mountain were detected in the Himalayas and Karakoram, however, few studies were carried out in the central Tibetan Plateau (TP). This study is focused on identification and characteristics of surge-type glaciers by using satellite InSAR technique on the Puruogangri Ice Field (PIF) in the central TP, the largest modern ice field over the TP. Firstly, a very high-resolution DEM was retrieved by applying bi-static InSAR to a pair of TerraSAR-X/Tandem-X data in 2012, then elevation changes were estimated by subtracting SRTM-X DEM (2000) from it. Secondly, bi-temporal surface velocities were measured by D-InSAR technique with a pair of ERS tandem data in 1996 and a pair of ALOS PALSAR data in 2009. The preliminary results of elevation changes show that a significant thickness increase of approximate 70 meters was detected at terminus of the glacier (WGMS id: 5Z213E0012) between 2000 and 2012. In particular, an analysis of glacier elevation changes with altitude exhibits that this glacier experienced a surging before 2012. Moreover, the results of surface velocity demonstrate that the ice-flow velocity amplitude of this glacier was relatively slow with average values of about 3.5 m/yr in 1996 and 3.0 m/yr in 2009. A synergistic analysis of the changes in elevation and velocity infers that the glacier surge event might occur between 1996 and 2009. But at the present we could not make sure of its exactly active and quiescent phase, and further studies are required.

Structural Basis for the Lesion-scanning Mechanism of the MutY DNA Glycosylase

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

Wang, Lan; Chakravarthy, Srinivas; Verdine, Gregory L.

The highly mutagenic A:8-oxoguanine (oxoG) base pair is generated mainly by misreplication of the C:oxoG base pair, the oxidation product of the C:G base pair. The A:oxoG base pair is particularly insidious because neither base in it carries faithful information to direct the repair of the other. The bacterial MutY (MUTYH in humans) adenine DNA glycosylase is able to initiate the repair of A:oxoG by selectively cleaving the A base from the A:oxoG base pair. The difference between faithful repair and wreaking mutagenic havoc on the genome lies in the accurate discrimination between two structurally similar base pairs: A:oxoG andmore » A:T. Here we present two crystal structures of the MutY N-terminal domain in complex with either undamaged DNA or DNA containing an intrahelical lesion. These structures have captured for the first time a DNA glycosylase scanning the genome for a damaged base in the very first stage of lesion recognition and the base extrusion pathway. The mode of interaction observed here has suggested a common lesion-scanning mechanism across the entire helix-hairpin-helix superfamily to which MutY belongs. In addition, small angle X-ray scattering studies together with accompanying biochemical assays have suggested a possible role played by the C-terminal oxoG-recognition domain of MutY in lesion scanning.« less

Intrafamilial variability in the clinical manifestations of mucopolysaccharidosis type II: Data from the Hunter Outcome Survey (HOS)

PubMed Central

Giugliani, Roberto; Harmatz, Paul; Mendelsohn, Nancy J.; Jego, Virginie; Parini, Rossella

2017-01-01

Several cases of phenotypic variability among family members with mucopolysaccharidosis type II (MPS II) have been reported, but the data are limited. Data from patients enrolled in the Hunter Outcome Survey (HOS) were used to investigate intrafamilial variability in male siblings with MPS II. As of July 2015, data were available for 78 patients aged ≥5 years at last visit who had at least one affected sibling (39 sibling pairs). These patients were followed prospectively (i.e., they were alive at enrollment in HOS). The median age at the onset of signs and symptoms was the same for the elder and younger brothers (2.0 years); however, the younger brothers were typically diagnosed at a younger age than the elder brothers (median age, 2.5 and 5.1 years, respectively). Of the 39 pairs, eight pairs were classified as being discordant (the status of four or more signs and symptoms differed between the siblings); 21 pairs had one, two, or three signs and symptoms that differed between the siblings, and 10 pairs had none. Regression status of the majority of the developmental milestones studied was generally concordant among siblings. Functional classification, a measure of central nervous system involvement, was the same in 24/28 pairs, although four pairs were considered discordant as functional classification differed between the siblings. Overall, this analysis revealed similarity in the clinical manifestations of MPS II among siblings. This information should help to improve our understanding of the clinical presentation of the disease, including phenotype prediction in affected family members. PMID:29210515

Phylogenetic Systematics, Biogeography, and Ecology of the Electric Fish Genus Brachyhypopomus (Ostariophysi: Gymnotiformes)

PubMed Central

de Santana, Carlos David; Waddell, Joseph C.; Lovejoy, Nathan R.

2016-01-01

A species-level phylogenetic reconstruction of the Neotropical bluntnose knifefish genus Brachyhypopomus (Gymnotiformes, Hypopomidae) is presented, based on 60 morphological characters, approximately 1100 base pairs of the mitochondrial cytb gene, and approximately 1000 base pairs of the nuclear rag2 gene. The phylogeny includes 28 species of Brachyhypopomus and nine outgroup species from nine other gymnotiform genera, including seven in the superfamily Rhamphichthyoidea (Hypopomidae and Rhamphichthyidae). Parsimony and Bayesian total evidence phylogenetic analyses confirm the monophyly of the genus, and identify nine robust species groups. Homoplastic osteological characters associated with diminutive body size and occurrence in small stream habitats, including loss of squamation and simplifications of the skeleton, appear to mislead a phylogenetic analysis based on morphological characters alone–resulting in the incorrect placing of Microsternarchus + Racenisia in a position deeply nested within Brachyhypopomus. Consideration of geographical distribution in light of the total evidence phylogeny indicates an origin for Brachyhypopomus in Greater Amazonia (the superbasin comprising the Amazon, Orinoco and major Guiana drainages), with subsequent dispersal and vicariance in peripheral basins, including the La Plata, the São Francisco, and trans-Andean basins of northwest South America and Central America. The ancestral habitat of Brachyhypopomus likely resembled the normoxic, low-conductivity terra firme stream system occupied by many extant species, and the genus has subsequently occupied a wide range of terra firme and floodplain habitats including low- and high-conductivity systems, and normoxic and hypoxic systems. Adaptations for impedance matching to high conductivity, and/or for air breathing in hypoxic systems have attended these habitat transitions. Several species of Brachyhypopomus are eurytopic with respect to habitat occupancy and these generally exhibit wider geographical ranges than stenotopic species. PMID:27736882

KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.

PubMed

Betz, Karin; Malyshev, Denis A; Lavergne, Thomas; Welte, Wolfram; Diederichs, Kay; Dwyer, Tammy J; Ordoukhanian, Phillip; Romesberg, Floyd E; Marx, Andreas

2012-07-01

Many candidate unnatural DNA base pairs have been developed, but some of the best-replicated pairs adopt intercalated structures in free DNA that are difficult to reconcile with known mechanisms of polymerase recognition. Here we present crystal structures of KlenTaq DNA polymerase at different stages of replication for one such pair, dNaM-d5SICS, and show that efficient replication results from the polymerase itself, inducing the required natural-like structure.

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

Egli, Martin; Pallan, Pradeep S.; Pattanayek, Rekha

An experimental rationalization of the structure type encountered in DNA and RNA by systematically investigating the chemical and physical properties of alternative nucleic acids has identified systems with a variety of sugar-phosphate backbones that are capable of Watson-Crick base pairing and in some cases cross-pairing with the natural nucleic acids. The earliest among the model systems tested to date, (4{prime} {yields} 6{prime})-linked oligo(2{prime},3{prime}-dideoxy-{beta}-d-glucopyranosyl)nucleotides or homo-DNA, shows stable self-pairing, but the pairing rules for the four natural bases are not the same as those in DNA. However, a complete interpretation and understanding of the properties of the hexapyranosyl (4{prime} {yields} 6{prime})more » family of nucleic acids has been impeded until now by the lack of detailed 3D-structural data. We have determined the crystal structure of a homo-DNA octamer. It reveals a weakly twisted right-handed duplex with a strong inclination between the hexose-phosphate backbones and base-pair axes, and highly irregular values for helical rise and twist at individual base steps. The structure allows a rationalization of the inability of allo-, altro-, and glucopyranosyl-based oligonucleotides to form stable pairing systems.« less

Sequence-dependent base pair stepping dynamics in XPD helicase unwinding

PubMed Central

Qi, Zhi; Pugh, Robert A; Spies, Maria; Chemla, Yann R

2013-01-01

Helicases couple the chemical energy of ATP hydrolysis to directional translocation along nucleic acids and transient duplex separation. Understanding helicase mechanism requires that the basic physicochemical process of base pair separation be understood. This necessitates monitoring helicase activity directly, at high spatio-temporal resolution. Using optical tweezers with single base pair (bp) resolution, we analyzed DNA unwinding by XPD helicase, a Superfamily 2 (SF2) DNA helicase involved in DNA repair and transcription initiation. We show that monomeric XPD unwinds duplex DNA in 1-bp steps, yet exhibits frequent backsteps and undergoes conformational transitions manifested in 5-bp backward and forward steps. Quantifying the sequence dependence of XPD stepping dynamics with near base pair resolution, we provide the strongest and most direct evidence thus far that forward, single-base pair stepping of a helicase utilizes the spontaneous opening of the duplex. The proposed unwinding mechanism may be a universal feature of DNA helicases that move along DNA phosphodiester backbones. DOI: http://dx.doi.org/10.7554/eLife.00334.001 PMID:23741615

Efficient Acceleration of the Pair-HMMs Forward Algorithm for GATK HaplotypeCaller on Graphics Processing Units.

PubMed

Ren, Shanshan; Bertels, Koen; Al-Ars, Zaid

2018-01-01

GATK HaplotypeCaller (HC) is a popular variant caller, which is widely used to identify variants in complex genomes. However, due to its high variants detection accuracy, it suffers from long execution time. In GATK HC, the pair-HMMs forward algorithm accounts for a large percentage of the total execution time. This article proposes to accelerate the pair-HMMs forward algorithm on graphics processing units (GPUs) to improve the performance of GATK HC. This article presents several GPU-based implementations of the pair-HMMs forward algorithm. It also analyzes the performance bottlenecks of the implementations on an NVIDIA Tesla K40 card with various data sets. Based on these results and the characteristics of GATK HC, we are able to identify the GPU-based implementations with the highest performance for the various analyzed data sets. Experimental results show that the GPU-based implementations of the pair-HMMs forward algorithm achieve a speedup of up to 5.47× over existing GPU-based implementations.

DNA bases ring-expanded with a cyclopentadiene free radical: a theoretical investigation of building blocks with diradical character.

PubMed

Zhao, Peiwen; Bu, Yuxiang

2016-01-14

In this work, we computationally design radical nucleobases which possess improved electronic properties, especially diradical properties through introducing a cyclopentadiene radical. We predict that the detailed electromagnetic features of base assemblies are based on the orientation of the extra five-membered cyclopentadiene ring. Broken symmetry DFT calculations take into account the relevant structures and properties. Our results reveal that both the radicalized DNA bases and the base pairs formed when they combine with their counterparts remain stable and display larger spin delocalization. The mode of embedding the cyclopentadiene free radical in the structures has some influence on the degree of π-conjugation, which results in various diradical characteristics. Single-layered radical base pairs all have an open-shell singlet ground state, but the energy difference between singlet and triplet is not significant. For two-layered radical base pairs, the situation is more complex. All of them have an open-shell state as their ground state, including an open-shell singlet state and an open-shell triplet state. That is, the majority of radical base pairs possess anti-ferromagnetic or ferromagnetic characteristics. We present here a more in-depth discussion and analyses to study the magnetic characteristics of radical bases and base pairs. As an important factor, two-layered radical base pairs also have been carefully analyzed. We hope that all the measurements and results presented here will stimulate further detailed insights into the related mechanisms in modified DNA bases and the design of better ring-expanded DNA magnetic materials.

Geochemistry of ferromanganese nodule-sediment pairs from Central Indian Ocean Basin

NASA Astrophysics Data System (ADS)

Pattan, J. N.; Parthiban, G.

2011-01-01

Fourteen ferromanganese nodule-sediment pairs from different sedimentary environments such as siliceous ooze (11), calcareous ooze (two) and red clay (one) from Central Indian Ocean Basin (CIOB) were analysed for major, trace and rare earth elements (REE) to understand the possible elemental relationship between them. Nodules from siliceous and calcareous ooze are diagenetic to early diagenetic whereas, nodule from red clay is of hydrogenetic origin. Si, Al and Ba are enriched in the sediments compared to associated nodules; K and Na are almost in the similar range in nodule-sediment pairs and Mn, Fe, Ti, Mg, P, Ni, Cu, Mo, Zn, Co, Pb, Sr, V, Y, Li and REEs are all enriched in nodules compared to associated sediments (siliceous and calcareous). Major portion of Si, Al and K in both nodules and sediments appear to be of terrigenous nature. The elements which are highly enriched in the nodules compared to associated sediments from both siliceous and calcareous ooze are Mo - (307, 273), Ni - (71, 125), Mn - (64, 87), Cu - (43, 80), Co - (23, 75), Pb - (15, 24), Zn - (9, 11) and V - (8, 19) respectively. These high enrichment ratios of elements could be due to effective diagenetic supply of metals from the underlying sediment to the nodule. Enrichment ratios of transition metals and REEs in the nodule to sediment are higher in CIOB compared to Pacific and Atlantic Ocean. Nodule from red clay, exhibit very small enrichment ratio of four with Mn and Ce while, Al, Fe, Ti, Ca, Na, K, Mg, P, Zn, Co, V, Y and REE are all enriched in red clay compared to associated nodule. This is probably due to presence of abundant smectite, fish teeth, micronodules and phillipsite in the red clay. The strong positive correlation ( r ⩾ 0.8) of Mn with Ni, Cu, Zn and Mo and a convex pattern of shale-normalized REE pattern with positive Ce-anomaly of siliceous ooze could be due to presence of abundant manganese micronodules. None of the major trace and REE exhibits any type of inter-elemental relationship between nodule and sediment pairs. Therefore, it may not be appropriate to correlate elemental behaviour between these pairs.

SU-E-T-335: Dosimetric Investigation of An Advanced Rotating Gamma Ray System for Imaged Guided Radiation Therapy

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

Ma, C; Eldib, A; Chibani, O

2015-06-15

Purpose: Co-60 beams have unique dosimetric properties for cranial treatments and thoracic cancers. The conventional concern about the high surface dose is overcome by modern system designs with rotational treatment techniques. This work investigates a novel rotational Gamma ray system for image-guided, external beam radiotherapy. Methods: The CybeRT system (Cyber Medical Corp., China) consists of a ring gantry with either one or two treatment heads containing a Gamma source and a multileaf collimator (MLC). The MLC has 60 paired leaves, and the maximum field size is either 40cmx40cm (40 pairs of 0.5cm central leaves, 20 pairs of 1cm outer leaves),more » or 22cmx40cm (32 pairs of 0.25cm central leaves, 28 pairs of 0.5cm outer leaves). The treatment head(s) can swing 35° superiorly and 8° inferiorly, allowing a total of 43° non-coplanar beam incident. The treatment couch provides 6-degrees-of-freedom motion compensation and the kV cone-beam CT system has a spatial resolution of 0.4mm. Monte Carlo simulations were used to compute dose distributions and compare with measurements. A retrospective study of 98 previously treated patients was performed to compare CybeRT with existing RT systems. Results: Monte Carlo results confirmed the CybeRT design parameters including output factors and 3D dose distributions. Its beam penumbra/dose gradient was similar to or better than that of 6MV photon beams and its isocenter accuracy is 0.3mm. Co-60 beams produce lower-energy secondary electrons that exhibit better dose properties in low-density lung tissues. Because of their rapid depth dose falloff, Co-60 beams are favorable for peripheral lung tumors with half-arc arrangements to spare the opposite lung and critical structures. Superior dose distributions were obtained for head and neck, breast, spine and lung tumors. Conclusion: Because of its accurate dose delivery and unique dosimetric properties of C-60 sources, CybeRT is ideally suited for advanced SBRT as well as conventional RT. This work was partially supported by Cyber Medical Corp.« less

Measurement of HbA1c in multicentre diabetes trials - should blood samples be tested locally or sent to a central laboratory: an agreement analysis.

PubMed

Arch, Barbara N; Blair, Joanne; McKay, Andrew; Gregory, John W; Newland, Paul; Gamble, Carrol

2016-10-24

Glycated haemoglobin (HbA1c) is an important outcome measure in diabetes clinical trials. For multicentre designs, HbA1c can be measured locally at participating centres or by sending blood samples to a central laboratory. This study analyses the agreement between local and central measurements, using 1-year follow-up data collected in a multicentre randomised controlled trial (RCT) of newly diagnosed children with type I diabetes. HbA1c measurements were routinely analysed both locally and centrally at baseline and then at 3, 6, 9 and 12 months and the data reported in mmol/mol. Agreement was assessed by calculating the bias and 95 % limits of agreement, using the Bland-Altman analysis method. A predetermined benchmark for clinically acceptable margin of error between measurements was subjectively set as ±10 % for HbA1c. The percentage of pairs of measurements that were classified as clinically acceptable was calculated. Descriptive statistics were used to examine the agreement within centres. Treatment group was not considered. Five hundred and ninety pairs of measurement, representing 255 children and 15 trial centres across four follow-up time points, were compared. There was no significant bias: local measurements were an average of 0.16 mmol/mol (SD = 4.5, 95 % CI -0.2 to 0.5) higher than central. The 95 % limits of agreement were -8.6 to 9.0 mmol/mol (local minus central). Eighty percent of local measurements were within ±10 % of corresponding central measurements. Some trial centres were more varied in the differences observed between local and central measurements: IQRs ranging from 3 to 9 mmol/mol; none indicated systematic bias. Variation in agreement between HbA1c measurements was greater than had been expected although no overall bias was detected and standard deviations were similar. Discrepancies were present across all participating centres. These findings have implications for the comparison of standards of clinical care between centres, the design of future multicentre RCTs and existing quality assurance processes for HbA1c measurements. We recommend that centralised HbA1c measurement is preferable in the multicentre clinical trial setting. Eudract No. 2010-023792-25 , registered on 4 November 2010.

Molecular dynamics study of some non-hydrogen-bonding base pair DNA strands

NASA Astrophysics Data System (ADS)

Tiwari, Rakesh K.; Ojha, Rajendra P.; Tiwari, Gargi; Pandey, Vishnudatt; Mall, Vijaysree

2018-05-01

In order to elucidate the structural activity of hydrophobic modified DNA, the DMMO2-D5SICS, base pair is introduced as a constituent in different set of 12-mer and 14-mer DNA sequences for the molecular dynamics (MD) simulation in explicit water solvent. AMBER 14 force field was employed for each set of duplex during the 200ns production-dynamics simulation in orthogonal-box-water solvent by the Particle-Mesh-Ewald (PME) method in infinite periodic boundary conditions (PBC) to determine conformational parameters of the complex. The force-field parameters of modified base-pair were calculated by Gaussian-code using Hartree-Fock /ab-initio methodology. RMSD Results reveal that the conformation of the duplex is sequence dependent and the binding energy of the complex depends on the position of the modified base-pair in the nucleic acid strand. We found that non-bonding energy had a significant contribution to stabilising such type of duplex in comparison to electrostatic energy. The distortion produced within strands by such type of base-pair was local and destabilised the duplex integrity near to substitution, moreover the binding energy of duplex depends on the position of substitution of hydrophobic base-pair and the DNA sequence and strongly supports the corresponding experimental study.

2-Methoxypyridine as a Thymidine Mimic in Watson-Crick Base Pairs of DNA and PNA: Synthesis, Thermal Stability, and NMR Structural Studies.

PubMed

Novosjolova, Irina; Kennedy, Scott D; Rozners, Eriks

2017-11-02

The development of nucleic acid base-pair analogues that use new modes of molecular recognition is important both for fundamental research and practical applications. The goal of this study was to evaluate 2-methoxypyridine as a cationic thymidine mimic in the A-T base pair. The hypothesis was that including protonation in the Watson-Crick base pairing scheme would enhance the thermal stability of the DNA double helix without compromising the sequence selectivity. DNA and peptide nucleic acid (PNA) sequences containing the new 2-methoxypyridine nucleobase (P) were synthesized and studied by using UV thermal melting and NMR spectroscopy. Introduction of P nucleobase caused a loss of thermal stability of ≈10 °C in DNA-DNA duplexes and ≈20 °C in PNA-DNA duplexes over a range of mildly acidic to neutral pH. Despite the decrease in thermal stability, the NMR structural studies showed that P-A formed the expected protonated base pair at pH 4.3. Our study demonstrates the feasibility of cationic unnatural base pairs; however, future optimization of such analogues will be required. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Radical-pair based avian magnetoreception

NASA Astrophysics Data System (ADS)

Procopio, Maria; Ritz, Thorsten

2014-03-01

Behavioural experiments suggest that migratory birds possess a magnetic compass sensor able to detect the direction of the geomagnetic. One hypothesis for the basis of this remarkable sensory ability is that the coherent quantum spin dynamics of photoinduced radical pair reactions transduces directional magnetic information from the geomagnetic field into changes of reaction yields, possibly involving the photoreceptor cryptochrome in the birds retina. The suggested radical-pair based avian magnetoreception has attracted attention in the field of quantum biology as an example of a biological sensor which might exploit quantum coherences for its biological function. Investigations on such a spin-based sensor have focussed on uncovering the design features for the design of a biomimetic magnetic field sensor. We study the effects of slow fluctuations in the nuclear spin environment on the directional signal. We quantitatively evaluate the robustness of signals under fluctuations on a timescale longer than the lifetime of a radical pair, utilizing two models of radical pairs. Our results suggest design principles for building a radical-pair based compass sensor that is both robust and highly directional sensitive.

From Mesocates to Helicates: Structural, Magnetic and Chiro-Optical Studies on Nickel(II) Supramolecular Assemblies Derived from Tetradentate Schiff Bases.

PubMed

Mayans, Júlia; Font-Bardia, Mercè; Di Bari, Lorenzo; Arrico, Lorenzo; Zinna, Francesco; Pescitelli, Gennaro; Escuer, Albert

2018-05-28

The systematic reactions of a family of tetradentate pyridyl/imine and quinolyl/imine racemic or enantiopure Schiff bases with Ni(NO 3 ) 2 or Ni(ClO 4 ) 2 in the presence of sodium azide yielded, as a function of the starting racemic, chiral or achiral base, a set of chiral, meso or achiral complexes. In all cases, the compounds consist of two Ni II cations linked by a double azido bridge in its end-on coordination mode. All the dimers exhibit a mesocate supramolecular structure and one of them, the unprecedented mix of helicate and mesocate in 2:1 ratio. The transition from mesocate to helicate conformation has been reached by tuning the flexibility of the central spacers of the Schiff bases and the size of the substituents. Electronic circular dichroism (ECD) studies have been performed for two pairs of enantiomers and interpreted by means of DFT calculations. Susceptibility measurements show a ferromagnetic coupling between the Ni II cations mediated by the end-on azido bridges. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Stringent Nucleotide Recognition by the Ribosome at the Middle Codon Position.

PubMed

Liu, Wei; Shin, Dongwon; Ng, Martin; Sanbonmatsu, Karissa Y; Tor, Yitzhak; Cooperman, Barry S

2017-08-29

Accurate translation of the genetic code depends on mRNA:tRNA codon:anticodon base pairing. Here we exploit an emissive, isosteric adenosine surrogate that allows direct measurement of the kinetics of codon:anticodon University of California base formation during protein synthesis. Our results suggest that codon:anticodon base pairing is subject to tighter constraints at the middle position than at the 5'- and 3'-positions, and further suggest a sequential mechanism of formation of the three base pairs in the codon:anticodon helix.

Characterization of the Trans Watson-Crick GU Base Pair Located in the Catalytic Core of the Antigenomic HDV Ribozyme

PubMed Central

Lévesque, Dominique; Reymond, Cédric; Perreault, Jean-Pierre

2012-01-01

The HDV ribozyme’s folding pathway is, by far, the most complex folding pathway elucidated to date for a small ribozyme. It includes 6 different steps that have been shown to occur before the chemical cleavage. It is likely that other steps remain to be discovered. One of the most critical of these unknown steps is the formation of the trans Watson-Crick GU base pair within loop III. The U23 and G28 nucleotides that form this base pair are perfectly conserved in all natural variants of the HDV ribozyme, and therefore are considered as being part of the signature of HDV-like ribozymes. Both the formation and the transformation of this base pair have been studied mainly by crystal structure and by molecular dynamic simulations. In order to obtain physical support for the formation of this base pair in solution, a set of experiments, including direct mutagenesis, the site-specific substitution of chemical groups, kinetic studies, chemical probing and magnesium-induced cleavage, were performed with the specific goal of characterizing this trans Watson-Crick GU base pair in an antigenomic HDV ribozyme. Both U23 and G28 can be substituted for nucleotides that likely preserve some of the H-bond interactions present before and after the cleavage step. The formation of the more stable trans Watson-Crick base pair is shown to be a post-cleavage event, while a possibly weaker trans Watson-Crick/Hoogsteen interaction seems to form before the cleavage step. The formation of this unusually stable post-cleavage base pair may act as a driving force on the chemical cleavage by favouring the formation of a more stable ground state of the product-ribozyme complex. To our knowledge, this represents the first demonstration of a potential stabilising role of a post-cleavage conformational switch event in a ribozyme-catalyzed reaction. PMID:22768274

Building a knowledge base of severe adverse drug events based on AERS reporting data using semantic web technologies.

PubMed

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

2013-01-01

A semantically coded knowledge base of adverse drug events (ADEs) with severity information is critical for clinical decision support systems and translational research applications. However it remains challenging to measure and identify the severity information of ADEs. The objective of the study is to develop and evaluate a semantic web based approach for building a knowledge base of severe ADEs based on the FDA Adverse Event Reporting System (AERS) reporting data. We utilized a normalized AERS reporting dataset and extracted putative drug-ADE pairs and their associated outcome codes in the domain of cardiac disorders. We validated the drug-ADE associations using ADE datasets from SIDe Effect Resource (SIDER) and the UMLS. We leveraged the Common Terminology Criteria for Adverse Event (CTCAE) grading system and classified the ADEs into the CTCAE in the Web Ontology Language (OWL). We identified and validated 2,444 unique Drug-ADE pairs in the domain of cardiac disorders, of which 760 pairs are in Grade 5, 775 pairs in Grade 4 and 2,196 pairs in Grade 3.

Demonstration of periodic nanostructure formation with less ablation by double-pulse laser irradiation on titanium

NASA Astrophysics Data System (ADS)

Furukawa, Yuki; Sakata, Ryoichi; Konishi, Kazuki; Ono, Koki; Matsuoka, Shusaku; Watanabe, Kota; Inoue, Shunsuke; Hashida, Masaki; Sakabe, Shuji

2016-06-01

By pairing femtosecond laser pulses (duration ˜40 fs and central wavelength ˜810 nm) at an appropriate time interval, a laser-induced periodic surface structure (LIPSS) is formed with much less ablation than one formed with a single pulse. On a titanium plate, a pair of laser pulses with fluences of 70 and 140 mJ/cm2 and a rather large time interval (>10 ps) creates a LIPSS with an interspace of 600 nm, the same as that formed by a single pulse of 210 mJ/cm2, while the double pulse ablates only 4 nm, a quarter of the ablation depth of a single pulse.

Quetzal: a transposon of the Tc1 family in the mosquito Anopheles albimanus.

PubMed

Ke, Z; Grossman, G L; Cornel, A J; Collins, F H

1996-10-01

A member of the Tc1 family of transposable elements has been identified in the Central and South American mosquito Anopheles albimanus. The full-length Quetzal element is 1680 base pairs (bp) in length, possesses 236 bp inverted terminal repeats (ITRs), and has a single open reading frame (ORF) with the potential of encoding a 341-amino-acid (aa) protein that is similar to the transposases of other members of the Tc1 family, particularly elements described from three different Drosophila species. The approximately 10-12 copies per genome of Quetzal are found in the euchromatin of all three chromosomes of A. albimanus. One full-length clone, Que27, appears capable of encoding a complete transposase and may represent a functional copy of this element.

The Vietnam Era Twin Registry: a resource for medical research.

PubMed Central

Henderson, W G; Eisen, S; Goldberg, J; True, W R; Barnes, J E; Vitek, M E

1990-01-01

The Vietnam Era Twin Registry consists of 4,774 male-male twin pairs born between 1939 and 1957 with both brothers having served in the United States military during the Vietnam War. The registry was originally developed to provide the best control group for Vietnam-exposed servicemen to study the long-term health consequences of service in Vietnam. Recognizing the potential value of the registry for other areas of medical research, the Department of Veterans Affairs in 1988 opened the registry for use by both VA and non-VA investigators. The existence of centralized VA data bases for deaths and VA hospitalizations will strengthen future followup of the twins. This article describes the characteristics of the registry population and the process for accessing the registry. PMID:2116638

Crystal structure of an Okazaki fragment at 2-A resolution

NASA Technical Reports Server (NTRS)

Egli, M.; Usman, N.; Zhang, S. G.; Rich, A.

1992-01-01

In DNA replication, Okazaki fragments are formed as double-stranded intermediates during synthesis of the lagging strand. They are composed of the growing DNA strand primed by RNA and the template strand. The DNA oligonucleotide d(GGGTATACGC) and the chimeric RNA-DNA oligonucleotide r(GCG)d(TATACCC) were combined to form a synthetic Okazaki fragment and its three-dimensional structure was determined by x-ray crystallography. The fragment adopts an overall A-type conformation with 11 residues per turn. Although the base-pair geometry, particularly in the central TATA part, is distorted, there is no evidence for a transition from the A- to the B-type conformation at the junction between RNA.DNA hybrid and DNA duplex. The RNA trimer may, therefore, lock the complete fragment in an A-type conformation.

Approximating Long-Term Statistics Early in the Global Precipitation Measurement Era

NASA Technical Reports Server (NTRS)

Stanley, Thomas; Kirschbaum, Dalia B.; Huffman, George J.; Adler, Robert F.

2017-01-01

Long-term precipitation records are vital to many applications, especially the study of extreme events. The Tropical Rainfall Measuring Mission (TRMM) has served this need, but TRMMs successor mission, Global Precipitation Measurement (GPM), does not yet provide a long-term record. Quantile mapping, the conversion of values across paired empirical distributions, offers a simple, established means to approximate such long-term statistics, but only within appropriately defined domains. This method was applied to a case study in Central America, demonstrating that quantile mapping between TRMM and GPM data maintains the performance of a real-time landslide model. Use of quantile mapping could bring the benefits of the latest satellite-based precipitation dataset to existing user communities such as those for hazard assessment, crop forecasting, numerical weather prediction, and disease tracking.

Terminal base pairs of oligodeoxynucleotides: imino proton exchange and fraying.

PubMed

Nonin, S; Leroy, J L; Guéron, M

1995-08-22

We have estimated the dissociation constant of the terminal base pairs of the B-DNA duplexes formed by 5'-d(CGCGATCGCG) and 5'-d(TAGCGCTA) by two methods, one based on the change in imino proton chemical shift with temperature and the other on the apparent pK shift of the imino proton, as monitored by the change in chemical shift of aromatic protons. These methods do not rely on imino proton exchange, whose rate was also measured. (1) The effect of ammonia on the imino proton exchange rate of the terminal pair of the 5'-d(CGCGATCGCG) duplex is 67 times less than on the isolated nucleoside. This provides an upper limit on the exchange rate from the closed pair. In fact, the effect is just as predicted from the dissociation constant, assuming that there is no exchange at all from the closed pair and that, as has been argued previously, external catalysts act on the open state as they do on the isolated nucleoside. The inhibition of catalyzed proton exchange in the closed pair, despite exposure of one face of the pair to solvent, is a new feature of the exchange process. It will allow determination of the dissociation constant of terminal pairs from the exchange rate. (2) Intrinsic catalysis of proton exchange is less efficient for the terminal pair than for an internal one. A possible explanation is that proton transfer across the water bridge responsible for intrinsic catalysis is slower, as expected if the open-state separation of the bases is larger in a terminal pair. This observation may lead to a direct method for the study of fraying. (3) At 0 degrees C, the dissociation constant of the second pair of the 5'-d(CGCGATCGCG) duplex is close to the square of the constant for the terminal pair, as predicted from a simple model of fraying. The enthalpy and entropy of opening of the terminal pairs may be compared with those of nearest neighbor interactions derived from calorimetry [Breslauer, K. J., et al. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 3746-3750].

Hybrid-denovo: a de novo OTU-picking pipeline integrating single-end and paired-end 16S sequence tags.

PubMed

Chen, Xianfeng; Johnson, Stephen; Jeraldo, Patricio; Wang, Junwen; Chia, Nicholas; Kocher, Jean-Pierre A; Chen, Jun

2018-03-01

Illumina paired-end sequencing has been increasingly popular for 16S rRNA gene-based microbiota profiling. It provides higher phylogenetic resolution than single-end reads due to a longer read length. However, the reverse read (R2) often has significant low base quality, and a large proportion of R2s will be discarded after quality control, resulting in a mixture of paired-end and single-end reads. A typical 16S analysis pipeline usually processes either paired-end or single-end reads but not a mixture. Thus, the quantification accuracy and statistical power will be reduced due to the loss of a large amount of reads. As a result, rare taxa may not be detectable with the paired-end approach, or low taxonomic resolution will result in a single-end approach. To have both the higher phylogenetic resolution provided by paired-end reads and the higher sequence coverage by single-end reads, we propose a novel OTU-picking pipeline, hybrid-denovo, that can process a hybrid of single-end and paired-end reads. Using high-quality paired-end reads as a gold standard, we show that hybrid-denovo achieved the highest correlation with the gold standard and performed better than the approaches based on paired-end or single-end reads in terms of quantifying the microbial diversity and taxonomic abundances. By applying our method to a rheumatoid arthritis (RA) data set, we demonstrated that hybrid-denovo captured more microbial diversity and identified more RA-associated taxa than a paired-end or single-end approach. Hybrid-denovo utilizes both paired-end and single-end 16S sequencing reads and is recommended for 16S rRNA gene targeted paired-end sequencing data.

Approximation for the Rayleigh Resolution of a Circular Aperture

ERIC Educational Resources Information Center

Mungan, Carl E.

2009-01-01

Rayleigh's criterion states that a pair of point sources are barely resolved by an optical instrument when the central maximum of the diffraction pattern due to one source coincides with the first minimum of the pattern of the other source. As derived in standard introductory physics textbooks, the first minimum for a rectangular slit of width "a"…

Christian Education, White Supremacy, and Humility in Formational Agendas

ERIC Educational Resources Information Center

Turpin, Katherine

2017-01-01

Christian education served as a tool of White supremacy that played a central role in the devastation of millions of human lives throughout the colonial era of Western expansion. An adequate account of how Christian education paired with colonial imperatives helps to identify where the legacy of White supremacy and imperial domination lives on in…

Language Aspects of Engineering Students' View of Entropy

ERIC Educational Resources Information Center

Haglund, Jesper; Andersson, Staffan; Elmgren, Maja

2016-01-01

Entropy is a central concept in thermodynamics, but has been found to be challenging to students due to its abstract nature and the fact that it is not part of students' everyday language. Interviews with three pairs of engineering students (N = 6) were conducted and video recorded regarding their interpretation and use of the entropy concept, one…

The Gasket of Circles: A Fractal of Circular Nature

ERIC Educational Resources Information Center

Haggar, Fred; Kricic, Senida

2017-01-01

Subdividing an equilateral triangle into four congruent triangles, then doing likewise to each of the three non-central triangles, and then again and again, leads to the Sierpinski gasket, from which the chaos game originated. An analogous procedure is hereforth applied to a circle, where a subdivision consists of two pairs of inscribed circles,…

"But, We Don't Have a Library": Exploring Approaches to Addressing Branch Campuses' Library Needs

ERIC Educational Resources Information Center

Hostetler, Kirsten; DeSilva, Michele

2016-01-01

Librarians at Central Oregon Community College's Barber Library explored how to best serve the needs of three satellite campuses across a large geographic region. While initially intending to start an embedded librarianship program, a pair of surveys showed the relationships and awareness necessary for the foundation of such a program were…

Interpreting landscape change: measured biophysical change and surrounding social context

Treesearch

Mimi M. Wagner; Paul H. Gobster

2007-01-01

Although research assessing both biophysical landscape conditions and social perceptions provide critical data on change, these methods are seldom integrated. In this study, we examined landscape change in the Central Iowa region by pairing quantitative data on changes to natural areas, streams, and housing density over the past 60 years with a qualitative social...

Above- and below-ground effects of aspen clonal regeneration and succession to conifers

Treesearch

Wayne D. Shepperd; Dale L. Bartos; Stephen A. Mata

2001-01-01

Above- and below-ground characteristics were measured and compared for six sets of paired trembling aspen (Populus tremuloides Michx.) clones on the Fishlake National Forest in central Utah. Three self-regenerating clones were compared with three non-regenerating clones and three pure aspen stands were compared with three mixed aspen-conifer stands. Regenerating clones...

Peripheral chemoreceptors tune inspiratory drive via tonic expiratory neuron hubs in the medullary ventral respiratory column network.

PubMed

Segers, L S; Nuding, S C; Ott, M M; Dean, J B; Bolser, D C; O'Connor, R; Morris, K F; Lindsey, B G

2015-01-01

Models of brain stem ventral respiratory column (VRC) circuits typically emphasize populations of neurons, each active during a particular phase of the respiratory cycle. We have proposed that "tonic" pericolumnar expiratory (t-E) neurons tune breathing during baroreceptor-evoked reductions and central chemoreceptor-evoked enhancements of inspiratory (I) drive. The aims of this study were to further characterize the coordinated activity of t-E neurons and test the hypothesis that peripheral chemoreceptors also modulate drive via inhibition of t-E neurons and disinhibition of their inspiratory neuron targets. Spike trains of 828 VRC neurons were acquired by multielectrode arrays along with phrenic nerve signals from 22 decerebrate, vagotomized, neuromuscularly blocked, artificially ventilated adult cats. Forty-eight of 191 t-E neurons fired synchronously with another t-E neuron as indicated by cross-correlogram central peaks; 32 of the 39 synchronous pairs were elements of groups with mutual pairwise correlations. Gravitational clustering identified fluctuations in t-E neuron synchrony. A network model supported the prediction that inhibitory populations with spike synchrony reduce target neuron firing probabilities, resulting in offset or central correlogram troughs. In five animals, stimulation of carotid chemoreceptors evoked changes in the firing rates of 179 of 240 neurons. Thirty-two neuron pairs had correlogram troughs consistent with convergent and divergent t-E inhibition of I cells and disinhibitory enhancement of drive. Four of 10 t-E neurons that responded to sequential stimulation of peripheral and central chemoreceptors triggered 25 cross-correlograms with offset features. The results support the hypothesis that multiple afferent systems dynamically tune inspiratory drive in part via coordinated t-E neurons. Copyright © 2015 the American Physiological Society.

Peripheral chemoreceptors tune inspiratory drive via tonic expiratory neuron hubs in the medullary ventral respiratory column network

PubMed Central

Segers, L. S.; Nuding, S. C.; Ott, M. M.; Dean, J. B.; Bolser, D. C.; O'Connor, R.; Morris, K. F.

2014-01-01

Models of brain stem ventral respiratory column (VRC) circuits typically emphasize populations of neurons, each active during a particular phase of the respiratory cycle. We have proposed that “tonic” pericolumnar expiratory (t-E) neurons tune breathing during baroreceptor-evoked reductions and central chemoreceptor-evoked enhancements of inspiratory (I) drive. The aims of this study were to further characterize the coordinated activity of t-E neurons and test the hypothesis that peripheral chemoreceptors also modulate drive via inhibition of t-E neurons and disinhibition of their inspiratory neuron targets. Spike trains of 828 VRC neurons were acquired by multielectrode arrays along with phrenic nerve signals from 22 decerebrate, vagotomized, neuromuscularly blocked, artificially ventilated adult cats. Forty-eight of 191 t-E neurons fired synchronously with another t-E neuron as indicated by cross-correlogram central peaks; 32 of the 39 synchronous pairs were elements of groups with mutual pairwise correlations. Gravitational clustering identified fluctuations in t-E neuron synchrony. A network model supported the prediction that inhibitory populations with spike synchrony reduce target neuron firing probabilities, resulting in offset or central correlogram troughs. In five animals, stimulation of carotid chemoreceptors evoked changes in the firing rates of 179 of 240 neurons. Thirty-two neuron pairs had correlogram troughs consistent with convergent and divergent t-E inhibition of I cells and disinhibitory enhancement of drive. Four of 10 t-E neurons that responded to sequential stimulation of peripheral and central chemoreceptors triggered 25 cross-correlograms with offset features. The results support the hypothesis that multiple afferent systems dynamically tune inspiratory drive in part via coordinated t-E neurons. PMID:25343784

Relativistic coupled cluster theory based on the no-pair Dirac-Coulomb-Breit Hamiltonian: Relativistic pair correlation energies of the Xe atom

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

Eliav, E.; Kaldor, U.; Ishikawa, Y.

1994-12-31

Relativistic pair correlation energies of Xe were computed by employing a recently developed relativistic coupled cluster theory based on the no-pair Dirac-Coulomb-Breit Hamiltonian. The matrix Dirac-Fock-Breit SCF and relativistic coupled cluster calculations were performed by means of expansion in basis sets of well-tempered Gaussian spinors. A detailed study of the pair correlation energies in Xe is performed, in order to investigate the effects of the low-frequency Breit interaction on the correlation energies of Xe. Nonadditivity of correlation and relativistic (particularly Breit) effects is discussed.

Central cavity of fructose-1,6-bisphosphatase and the evolution of AMP/fructose 2,6-bisphosphate synergism in eukaryotic organisms.

PubMed

Gao, Yang; Shen, Lu; Honzatko, Richard B

2014-03-21

The effects of AMP and fructose 2,6-bisphosphate (Fru-2,6-P2) on porcine fructose-1,6-bisphosphatase (pFBPase) and Escherichia coli FBPase (eFBPase) differ in three respects. AMP/Fru-2,6-P2 synergism in pFBPase is absent in eFBPase. Fru-2,6-P2 induces a 13° subunit pair rotation in pFBPase but no rotation in eFBPase. Hydrophilic side chains in eFBPase occupy what otherwise would be a central aqueous cavity observed in pFBPase. Explored here is the linkage of AMP/Fru-2,6-P2 synergism to the central cavity and the evolution of synergism in FBPases. The single mutation Ser(45) → His substantially fills the central cavity of pFBPase, and the triple mutation Ser(45) → His, Thr(46) → Arg, and Leu(186) → Tyr replaces porcine with E. coli type side chains. Both single and triple mutations significantly reduce synergism while retaining other wild-type kinetic properties. Similar to the effect of Fru-2,6-P2 on eFBPase, the triple mutant of pFBPase with bound Fru-2,6-P2 exhibits only a 2° subunit pair rotation as opposed to the 13° rotation exhibited by the Fru-2,6-P2 complex of wild-type pFBPase. The side chain at position 45 is small in all available eukaryotic FBPases but large and hydrophilic in bacterial FBPases, similar to eFBPase. Sequence information indicates the likelihood of synergism in the FBPase from Leptospira interrogans (lFBPase), and indeed recombinant lFBPase exhibits AMP/Fru-2,6-P2 synergism. Unexpectedly, however, AMP also enhances Fru-6-P binding to lFBPase. Taken together, these observations suggest the evolution of AMP/Fru-2,6-P2 synergism in eukaryotic FBPases from an ancestral FBPase having a central aqueous cavity and exhibiting synergistic feedback inhibition by AMP and Fru-6-P.

Organization of the central control of muscles of facial expression in man

PubMed Central

Root, A A; Stephens, J A

2003-01-01

Surface EMGs were recorded simultaneously from ipsilateral pairs of facial muscles while subjects made three different common facial expressions: the smile, a sad expression and an expression of horror, and three contrived facial expressions. Central peaks were found in the cross-correlograms of EMG activity recorded from the orbicularis oculi and zygomaticus major during smiling, the corrugator and depressor anguli oris during the sad look and the frontalis and mentalis during the horror look. The size of the central peak was significantly greater between the orbicularis oculi and zygomaticus major during smiling. It is concluded that co-contraction of facial muscles during some facial expressions are accompanied by the presence of common synaptic drive to the motoneurones supplying the muscles involved. Central peaks were found in the cross-correlograms of EMG activity recorded from the frontalis and depressor anguli oris during a contrived expression. However, no central peaks were found in the cross-correlograms of EMG activity recorded from the frontalis and orbicularis oculi or from the frontalis and zygomaticus major during the other two contrived expressions. It is concluded that a common synaptic drive is not present between all possible facial muscle pairs and suggests a functional role for the synergy. The origin of the common drive is discussed. It is concluded that activity in branches of common stem last-order presynaptic input fibres to motoneurones innervating the different facial muscles and presynaptic synchronization of input activity to the different motoneurone pools is involved. The former probably contributes more to the drive to the orbicularis oculi and zygomaticus major during smiling, while the latter is probably more prevalent in the corrugator and depressor anguli oris during the sad look, the frontalis and mentalis during the horror look and the frontalis and depressor anguli oris during one of the contrived expressions. The strength of common synaptic drive is inversely related to the degree of separate control that can be exhibited by the facial muscles involved. PMID:12692176

On twelve types of covering-based rough sets.

PubMed

Safari, Samira; Hooshmandasl, Mohammad Reza

2016-01-01

Covering approximation spaces are a generalization of equivalence-based rough set theories. In this paper, we will consider twelve types of covering based approximation operators by combining four types of covering lower approximation operators and three types of covering upper approximation operators. Then, we will study the properties of these new pairs and show they have most of the common properties among existing covering approximation pairs. Finally, the relation between these new pairs is studied.

Evidence for Watson-Crick and not Hoogsteen or wobble base pairing in the selection of nucleotides for insertion opposite pyrimidines and a thymine dimer by yeast DNA pol eta.

PubMed

Hwang, Hanshin; Taylor, John-Stephen

2005-03-29

We have recently reported that pyrene nucleotide is preferentially inserted opposite an abasic site, the 3'-T of a thymine dimer, and most undamaged bases by yeast DNA polymerase eta (pol eta). Because pyrene is a nonpolar molecule with no H-bonding ability, the unusually high efficiencies of dPMP insertion are ascribed to its superior base stacking ability, and underscore the importance of base stacking in the selection of nucleotides by pol eta. To investigate the role of H-bonding and base pair geometry in the selection of nucleotides by pol eta, we determined the insertion efficiencies of the base-modified nucleotides 2,6-diaminopurine, 2-aminopurine, 6-chloropurine, and inosine which would make a different number of H-bonds with the template base depending on base pair geometry. Watson-Crick base pairing appears to play an important role in the selection of nucleotide analogues for insertion opposite C and T as evidenced by the decrease in the relative insertion efficiencies with a decrease in the number of Watson-Crick H-bonds and an increase in the number of donor-donor and acceptor-acceptor interactions. The selectivity of nucleotide insertion is greater opposite the 5'-T than the 3'-T of the thymine dimer, in accord with previous work suggesting that the 5'-T is held more rigidly than the 3'-T. Furthermore, insertion of A opposite both Ts of the dimer appears to be mediated by Watson-Crick base pairing and not by Hoogsteen base pairing based on the almost identical insertion efficiencies of A and 7-deaza-A, the latter of which lacks H-bonding capability at N7. The relative efficiencies for insertion of nucleotides that can form Watson-Crick base pairs parallel those for the Klenow fragment, whereas the Klenow fragment more strongly discriminates against mismatches, in accord with its greater shape selectivity. These results underscore the importance of H-bonding and Watson-Crick base pair geometry in the selection of nucleotides by both pol eta and the Klenow fragment, and the lesser role of shape selection in insertion by pol eta due to its more open and less constrained active site.

Rice agriculture impacts catchment hydrographic patterns and nitrogen export characteristics in subtropical central China: a paired-catchment study.

PubMed

Wang, Yi; Liu, Xinliang; Wang, Hua; Li, Yong; Li, Yuyuan; Liu, Feng; Xiao, Runlin; Shen, Jianlin; Wu, Jinshui

2017-06-01

Increased nitrogen (N) concentrations in water bodies have highlighted issues regarding nutrient pollution in agricultural catchments. In this study, the ammonium-N (NH 4 + -N), nitrate-N (NO 3 - -N), and total N (TN) concentrations were observed in the stream water and groundwater of two contrasting catchments (named Tuojia and Jianshan) in subtropical central China from 2010 to 2014, to determine the rice agriculture impacts on the hydrographic patterns, and N export characteristics of the catchments. The results suggested that greater amounts of stream flow (523.0 vs. 434.7 mm year -1 ) and base flow (237.6 vs. 142.8 mm year -1 ) were produced in Tuojia than in Jianshan, and a greater base flow contribution to stream flow and higher frequencies of high-base flow days were observed during the fallow season than during the rice-growing season, indicating that intensive rice agriculture strongly influences the catchment hydrographic pattern. Rice agriculture resulted in moderate N pollution in the stream water and groundwater, particularly in Tuojia. Primarily, rice agriculture increased the NH 4 + -N concentration in the stream water; however, it increased the NO 3 - -N concentrations in the groundwater, suggesting that the different N species in the paddy fields migrated out of the catchments through distinct hydrological pathways. The average TN loading via stream flow and base flow was greater in Tuojia than in Jianshan (1.72 and 0.58 vs. 0.72 and 0.15 kg N ha -1  month -1 , respectively). Greater TN loading via stream flow was observed during the fallow season in Tuojia and during the rice-growing season in Jianshan, and these different results were most likely a result of the higher base flow contribution to TN loading (33.5 vs. 21.3%) and greater base flow enrichment ratio (1.062 vs. 0.876) in Tuojia than in Jianshan. Therefore, the impact of rice agriculture on catchment eco-hydrological processes should be considered when performing water quality protection and treatment in subtropical central China.