| 1. |
- Adare, A., et al.
(author)
-
Photon-hadron jet correlations in p plus p and Au plus Au collisions at s(NN)=200 GeV
- 2009
-
In: Physical Review C (Nuclear Physics). - 0556-2813. ; 80:2
-
Journal article (peer-reviewed)abstract
- We report the observation at the Relativistic Heavy Ion Collider of suppression of back-to-back correlations in the direct photon+jet channel in Au+Au relative to p+p collisions. Two-particle correlations of direct photon triggers with associated hadrons are obtained by statistical subtraction of the decay photon-hadron (gamma-h) background. The initial momentum of the away-side parton is tightly constrained, because the parton-photon pair exactly balance in momentum at leading order in perturbative quantum chromodynamics, making such correlations a powerful probe of the in-medium parton energy loss. The away-side nuclear suppression factor, I-AA, in central Au+Au collisions, is 0.32 +/- 0.12(stat)+/- 0.09(syst) for hadrons of 3 < p(T)(h)< 5 in coincidence with photons of 5 < p(T)(gamma)< 15 GeV/c. The suppression is comparable to that observed for high-p(T) single hadrons and dihadrons. The direct photon associated yields in p+p collisions scale approximately with the momentum balance, z(T)equivalent to p(T)(h)/p(T)(gamma), as expected for a measurement of the away-side parton fragmentation function. We compare to Au+Au collisions for which the momentum balance dependence of the nuclear modification should be sensitive to the path-length dependence of parton energy loss.
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| 2. |
- Adare, A., et al.
(author)
-
Charged hadron multiplicity fluctuations in Au plus Au and Cu plus Cu collisions from s(NN)=22.5 to 200 GeV
- 2008
-
In: Physical Review C (Nuclear Physics). - 0556-2813. ; 78:4
-
Journal article (peer-reviewed)abstract
- A comprehensive survey of event-by-event fluctuations of charged hadron multiplicity in relativistic heavy ions is presented. The survey covers Au+Au collisions at s(NN)=62.4 and 200 GeV, and Cu+Cu collisions at s(NN)=22.5,62.4, and 200 GeV. Fluctuations are measured as a function of collision centrality, transverse momentum range, and charge sign. After correcting for nondynamical fluctuations due to fluctuations in the collision geometry within a centrality bin, the remaining dynamical fluctuations expressed as the variance normalized by the mean tend to decrease with increasing centrality. The dynamical fluctuations are consistent with or below the expectation from a superposition of participant nucleon-nucleon collisions based upon p+p data, indicating that this dataset does not exhibit evidence of critical behavior in terms of the compressibility of the system. A comparison of the data with a model where hadrons are independently emitted from a number of hadron clusters suggests that the mean number of hadrons per cluster is small in heavy ion collisions.
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| 3. |
- Adare, A., et al.
(author)
-
System size and energy dependence of jet-induced hadron pair correlation shapes in Cu+Cu and Au+Au collisions at root S-NN 200 and 62.4 GeV
- 2007
-
In: Physical Review Letters. - 1079-7114. ; 98:23
-
Journal article (peer-reviewed)abstract
- We present azimuthal angle correlations of intermediate transverse momentum (1-4 GeV/c) hadrons from dijets in Cu+Cu and Au+Au collisions at root s(NN)=62.4 and 200 GeV. The away-side dijet induced azimuthal correlation is broadened, non-Gaussian, and peaked away from Delta phi=pi in central and semicentral collisions in all the systems. The broadening and peak location are found to depend upon the number of participants in the collision, but not on the collision energy or beam nuclei. These results are consistent with sound or shock wave models, but pose challenges to Cherenkov gluon radiation models.
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| 4. |
- Adare, A., et al.
(author)
-
Correlated production of p and (p)over-bar in Au+Au collisions at root s(NN)=200 GeV
- 2007
-
In: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 649:5-6, s. 359-369
-
Journal article (peer-reviewed)abstract
- Correlations between p and (p) over bar at transverse momenta typical of enhanced baryon production in Au + Au collisions are reported. The PHENIX experiment has measured same and opposite sign baryon pairs in Au + Au collisions at root s(NN) = 200 GeV. Correlated production of p and p with the trigger particle from the range 2.5 < p(T) < 4.0 GeV/c and the associated particle with 1.8 < p(T) < 2.5 GeV/c is observed to be nearly independent of the centrality of the collisions. Same sign pairs show no correlation at any centrality. The conditional yield of mesons triggered by baryons (and anti-baryons) and mesons in the same p(T) range rises with increasing centrality, except for the most central collisions, where baryons show a significantly smaller number of associated mesons. These data are consistent with a picture in which hard scattered partons produce correlated p and (p) over bar in the p(T) region of the baryon excess. (c) 2007 Elsevier B.V. All rights reserved.
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| 5. |
- Adare, A., et al.
(author)
-
Dihadron azimuthal correlations in Au+Au collisions at root s(NN)=200 GeV
- 2008
-
In: Physical Review C (Nuclear Physics). - 0556-2813. ; 78:1
-
Journal article (peer-reviewed)abstract
- Azimuthal angle (Delta phi) correlations are presented for a broad range of transverse momentum (0.4 < p(T) < 10 GeV/c) and centrality (0-92%) selections for charged hadrons from dijets in Au+Au collisions at root s(NN) = 200 GeV. With increasing p(T), the away-side Delta phi distribution evolves from a broad and relatively flat shape to a concave shape, then to a convex shape. Comparisons with p + p data suggest that the away-side distribution can be divided into a partially suppressed "head" region centered at Delta phi similar to pi, and an enhanced "shoulder" region centered at Delta phi similar to pi +/- 1.1. The p(T) spectrum for the associated hadrons in the head region softens toward central collisions. The spectral slope for the shoulder region is independent of centrality and trigger p(T). The properties of the near-side distributions are also modified relative to those in p + p collisions, reflected by the broadening of the jet shape in Delta phi and Delta eta, and an enhancement of the per-trigger yield. However, these modifications seem to be limited to p(T)less than or similar to 4 GeV/c, above which both the hadron pair shape and per-trigger yield become similar to p + p collisions. These observations suggest that both the away- and near-side distributions contain a jet fragmentation component which dominates for p(T) greater than or similar to 5 GeV/c and a medium-induced component which is important for p(T) less than or similar to 4 GeV/c. We also quantify the role of jets at intermediate and low p(T) through the yield of jet-induced pairs in comparison with binary scaled p + p pair yield. The yield of jet-induced pairs is suppressed at high pair proxy energy (sum of the p(T) magnitudes of the two hadrons) and is enhanced at low pair proxy energy. The former is consistent with jet quenching; the latter is consistent with the enhancement of soft hadron pairs due to transport of lost energy to lower p(T).
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| 6. |
- Adare, A., et al.
(author)
-
Energy loss and flow of heavy quarks in Au+Au collisions at root s(NN) = 200 GeV
- 2007
-
In: Physical Review Letters. - 1079-7114. ; 98:17
-
Journal article (peer-reviewed)abstract
- The PHENIX experiment at the BNL Relativistic Heavy Ion Collider (RHIC) has measured electrons with 0.3 < p(T) < 9 GeV/c at midrapidity (y < 0.35) from heavy-flavor (charm and bottom) decays in Au + Au collisions at root s(NN) = 200 GeV. The nuclear modification factor R-AA relative to p + p collisions shows a strong suppression in central Au + Au collisions, indicating substantial energy loss of heavy quarks in the medium produced at RHIC energies. A large azimuthal anisotropy v(2) with respect to the reaction plane is observed for 0.5 < p(T) < 5 GeV/c indicating substantial heavy-flavor elliptic flow. Both R-AA and v(2) show a p(T) dependence different from those of neutral pions. A comparison to transport models which simultaneously describe R-AA(p(T)) and v(2)(p(T)) suggests that the viscosity to entropy density ratio is close to the conjectured quantum lower bound, i.e., near a perfect fluid.
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| 7. |
- Adare, A., et al.
(author)
-
J/psi production versus centrality, transverse momentum, and rapidity in Au+Au collisions at root S(NN) = 200 GeV
- 2007
-
In: Physical Review Letters. - 1079-7114. ; 98:23
-
Journal article (peer-reviewed)abstract
- The PHENIX experiment at the BNL Relativistic Heavy Ion Collider (RHIC) has measured J/psi production for rapidities -2.2 < y < 2.2 in Au+Au collisions at root s(NN)=200 GeV. The J/psi invariant yield and nuclear modification factor R-AA as a function of centrality, transverse momentum, and rapidity are reported. A suppression of J/psi relative to binary collision scaling of proton-proton reaction yields is observed. Models which describe the lower energy J/psi data at the CERN Super Proton Synchrotron invoking only J/psi destruction based on the local medium density predict a significantly larger suppression at RHIC and more suppression at midrapidity than at forward rapidity. Both trends are contradicted by our data.
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| 8. |
- Adare, A., et al.
(author)
-
Quantitative constraints on the transport properties of hot partonic matter from semi-inclusive single high transverse momentum pion suppression in Au plus Au collisions at root S-NN=200 GeV
- 2008
-
In: Physical Review C (Nuclear Physics). - 0556-2813. ; 77:6
-
Journal article (peer-reviewed)abstract
- The PHENIX experiment has measured the suppression of semi-inclusive single high-transverse-momentum pi(0)'s in Au+Au collisions at root s(NN) = 200 GeV. The present understanding of this suppression is in terms of energy loss of the parent (fragmenting) parton in a dense color-charge medium. We have performed a quantitative comparison between various parton energy-loss models and our experimental data. The statistical point-to-point uncorrelated as well as correlated systematic uncertainties are taken into account in the comparison. We detail this methodology and the resulting constraint on the model parameters, such as the initial color-charge density dN(g)/dy, the medium transport coefficient <(q) over cap >, or the initial energy-loss parameter epsilon(0). We find that high-transverse-momentum pi(0) suppression in Au+Au collisions has sufficient precision to constrain these model-dependent parameters at the +/- 20-25% (one standard deviation) level. These constraints include only the experimental uncertainties, and further studies are needed to compute the corresponding theoretical uncertainties.
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| 9. |
- Adare, A., et al.
(author)
-
Scaling properties of azimuthal anisotropy in Au plus Au and Cu plus Cu collisions at root s(NN)=200 GeV
- 2007
-
In: Physical Review Letters. - 1079-7114. ; 98:16
-
Journal article (peer-reviewed)abstract
- Differential measurements of elliptic flow (v(2)) for Au+Au and Cu+Cu collisions at root s(NN)=200 GeV are used to test and validate predictions from perfect fluid hydrodynamics for scaling of v(2) with eccentricity, system size, and transverse kinetic energy (KET). For KET equivalent to m(T)-m up to similar to 1 GeV the scaling is compatible with hydrodynamic expansion of a thermalized fluid. For large values of KET mesons and baryons scale separately. Quark number scaling reveals a universal scaling of v(2) for both mesons and baryons over the full KET range for Au+Au. For Au+Au and Cu+Cu the scaling is more pronounced in terms of KET, rather than transverse momentum.
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| 10. |
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| 11. |
- Adare, A., et al.
(author)
-
Transverse momentum and centrality dependence of dihadron correlations in Au plus Au collisions at root s(NN)=200 GeV: Jet quenching and the response of partonic matter
- 2008
-
In: Physical Review C (Nuclear Physics). - 0556-2813. ; 77:1, s. 6-011901
-
Journal article (peer-reviewed)abstract
- Azimuthal angle (Delta phi) correlations are presented for charged hadrons from dijets for 0.4 < p(T)< 10 GeV/c in Au+Au collisions at root s(NN)=200 GeV. With increasing p(T), the away-side distribution evolves from a broad and relatively flat shape to a concave shape, then to a convex shape. Comparisons to p+p data suggest that the away-side can be divided into a partially suppressed "head" region centered at Delta phi similar to pi and an enhanced "shoulder" region centered at Delta phi similar to pi +/- 1.1. The p(T) spectrum for the head region softens toward central collisions, consistent with the onset of jet quenching. The spectral slope for the shoulder region is independent of centrality and trigger p(T), which offers constraints on energy transport mechanisms and suggests that it contains the medium response to energetic jets.
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| 12. |
- Afanasiev, S., et al.
(author)
-
Charged Kaon Interferometric Probes of Space-Time Evolution in Au plus Au Collisions at s(NN)=200 GeV
- 2009
-
In: Physical Review Letters. - 1079-7114. ; 103:14
-
Journal article (peer-reviewed)abstract
- Bose-Einstein correlations of charged kaons are used to probe Au+Au collisions at s(NN)=200 GeV and are compared to charged pion probes, which have a larger hadronic scattering cross section. Three-dimensional Gaussian source radii are extracted, along with a one-dimensional kaon emission source function. The centrality dependences of the three Gaussian radii are well described by a single linear function of N-part(1/3) with a zero intercept. Imaging analysis shows a deviation from a Gaussian tail at r greater than or similar to 10 fm, although the bulk emission at lower radius is well described by a Gaussian. The presence of a non-Gaussian tail in the kaon source reaffirms that the particle emission region in a heavy-ion collision is extended, and that similar measurements with pions are not solely due to the decay of long-lived resonances.
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| 13. |
- Afanasiev, S., et al.
(author)
-
Elliptic flow for phi mesons and (Anti)deuterons in Au+Au collisions at root s(NN)=200 GeV
- 2007
-
In: Physical Review Letters. - 1079-7114. ; 99:5
-
Journal article (peer-reviewed)abstract
- Differential elliptic flow (v(2)) for phi mesons and (anti)deuterons ((d) over bar )d is measured for Au + Au collisions at root s(NN) = 200 GeV. The v(2) for phi mesons follows the trend of lighter pi(+/-) and K-+/- mesons, suggesting that ordinary hadrons interacting with standard hadronic cross sections are not the primary driver for elliptic flow development. The v(2) values for ((d) over bar )d suggest that elliptic flow is additive for composite particles. This further validation of the universal scaling of v(2) per constituent quark for baryons and mesons suggests that partonic collectivity dominates the transverse expansion dynamics.
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| 14. |
- Afanasiev, S., et al.
(author)
-
High-p(T) pi(0) production with respect to the reaction plane in Au plus Au collisions at s(NN)=200 GeV
- 2009
-
In: Physical Review C (Nuclear Physics). - 0556-2813. ; 80:5
-
Journal article (peer-reviewed)abstract
- Measurements of the azimuthal anisotropy of high-p(T) neutral pion (pi(0)) production in Au+Au collisions at s(NN)=200 GeV by the PHENIX experiment are presented. The data included in this article were collected during the 2004 Relativistic Heavy Ion Collider running period and represent approximately an order of magnitude increase in the number of analyzed events relative to previously published results. Azimuthal angle distributions of pi(0) mesons detected in the PHENIX electromagnetic calorimeters are measured relative to the reaction plane determined event-by-event using the forward and backward beam-beam counters. Amplitudes of the second Fourier component (v(2)) of the angular distributions are presented as a function of pi(0) transverse momentum (p(T)) for different bins in collision centrality. Measured reaction plane dependent pi(0) yields are used to determine the azimuthal dependence of the pi(0) suppression as a function of p(T), R-AA(Delta phi,p(T)). A jet-quenching motivated geometric analysis is presented that attempts to simultaneously describe the centrality dependence and reaction plane angle dependence of the pi(0) suppression in terms of the path lengths of hypothetical parent partons in the medium. This set of results allows for a detailed examination of the influence of geometry in the collision region and of the interplay between collective flow and jet-quenching effects along the azimuthal axis.
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| 15. |
- Afanasiev, S., et al.
(author)
-
Particle-species dependent modification of jet-induced correlations in Au plus Au collisions at root s(NN)=200 GeV
- 2008
-
In: Physical Review Letters. - 1079-7114. ; 101:8
-
Journal article (peer-reviewed)abstract
- Measurements in Au + Au collisions at root s(NN) = 200 GeV of jet correlations for a trigger hadron at intermediate transverse momentum (p(T,trig)) with associated mesons or baryons at lower p(T,assoc) indicate strong modification of the away-side jet. The ratio of jet-associated baryons to mesons increases with centrality and p(T,assoc). For the most central collisions, the ratio is similar to that for inclusive measurements. This trend is incompatible with in-vacuum fragmentation but could be due to jetlike contributions from correlated soft partons, which recombine upon hadronization.
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| 16. |
- Afanasiev, S., et al.
(author)
-
Photoproduction of J/psi and of high mass e(+)e(-) in ultra-peripheral Au plus Au collisions at root s(NN)=200 GeV
- 2009
-
In: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 679:4, s. 321-329
-
Journal article (peer-reviewed)abstract
- We present the first measurement of photoproduction of J/psi and of two-photon production of high-mass e(+)e(-) pairs in electromagnetic (or ultra-peripheral) nucleus-nucleus interactions, using Au + Au data at root s(NN) = 200 GeV. The events are tagged with forward neutrons emitted following Coulomb excitation of one or both Au* nuclei. The event sample consists of 28 events with m(e+e-) > 2 GeV/c(2) with zero like-sign background. The measured cross sections at midrapidity of d sigma/dy (J/psi + Xn, y = 0) = 76 +/- 33 (stat) +/- 11 (syst) pb and d(2)sigma /dm dy (e(+) e(-) + Xn, y = 0) = 86 +/- 23(stat) +/- 16(syst) mu b/ (GeV/c(2)) for m(e+e-) epsilon vertical bar 2.0, 2.8 vertical bar GeV/c(2) have been compared and found to be consistent with models for photoproduction of J/psi and QED based calculations of two-photon production of e(+)e(-) pairs. (C) 2009 Elsevier B.V. All rights reserved.
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| 17. |
- Afanasiev, S., et al.
(author)
-
Source breakup dynamics in Au+Au collisions at root s(NN)=200 GeV via three-dimensional two-pion source imaging
- 2008
-
In: Physical Review Letters. - 1079-7114. ; 100:23
-
Journal article (peer-reviewed)abstract
- A three-dimensional correlation function obtained from midrapidity, low p(T), pion pairs in central Au+Au collisions at root s(NN) = 200 GeV is studied. The extracted model-independent source function indicates a long range tail in the directions of the pion pair transverse momentum (out) and the beam (long). A proper breakup time tau(0) similar to 9 fm/c and a mean proper emission duration Delta tau similar to 2 fm/c, leading to sizable emission time differences ( approximate to 12 fm/c), are required to allow models to be successfully matched to these tails. The model comparisons also suggest an outside-in "burning" of the emission source reminiscent of many hydrodynamical models.
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| 18. |
- Afanasiev, S., et al.
(author)
-
Systematic studies of elliptic flow measurements in Au plus Au collisions at s(NN)=200 GeV
- 2009
-
In: Physical Review C (Nuclear Physics). - 0556-2813. ; 80:2
-
Journal article (peer-reviewed)abstract
- We present inclusive charged hadron elliptic flow (v(2)) measured over the pseudorapidity range vertical bar eta vertical bar < 0.35 in Au+Au collisions at s(NN)=200 GeV. Results for v(2) are presented over a broad range of transverse momentum (p(T)=0.2-8.0 GeV/c) and centrality (0-60%). To study nonflow effects that are correlations other than collective flow, as well as the fluctuations of v(2), we compare two different analysis methods: (1) the event-plane method from two independent subdetectors at forward (vertical bar eta vertical bar=3.1-3.9) and beam (vertical bar eta vertical bar>6.5) pseudorapidities and (2) the two-particle cumulant method extracted using correlations between particles detected at midrapidity. The two event-plane results are consistent within systematic uncertainties over the measured p(T) and in centrality 0-40%. There is at most a 20% difference in the v(2) between the two event-plane methods in peripheral (40-60%) collisions. The comparisons between the two-particle cumulant results and the standard event-plane measurements are discussed.
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| 19. |
- Abate, E., et al.
(author)
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Combined performance tests before installation of the ATLAS Semiconductor and Transition Radiation Tracking Detectors
- 2008
-
In: Journal of Instrumentation. - 1748-0221. ; 3
-
Journal article (peer-reviewed)abstract
- The ATLAS (A Toroidal LHC ApparatuS) Inner Detector provides charged particle tracking in the centre of the ATLAS experiment at the Large Hadron Collider (LHC). The Inner Detector consists of three subdetectors: the Pixel Detector, the Semiconductor Tracker (SCT), and the Transition Radiation Tracker (TRT). This paper summarizes the tests that were carried out at the final stage of SCT+TRT integration prior to their installation in ATLAS. The combined operation and performance of the SCT and TRT barrel and endcap detectors was investigated through a series of noise tests, and by recording the tracks of cosmic rays. This was a crucial test of hardware and software of the combined tracker detector systems. The results of noise and cross-talk tests on the SCT and TRT in their final assembled configuration, using final readout and supply hardware and software, are reported. The reconstruction and analysis of the recorded cosmic tracks allowed testing of the offline analysis chain and verification of basic tracker performance parameters, such as efficiency and spatial resolution, in combined operation before installation.
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| 20. |
- Adcox, K, et al.
(author)
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Formation of dense partonic matter in relativistic nucleus-nucleus collisions at RHIC: Experimental evaluation by the PHENIX Collaboration
- 2005
-
In: Nuclear Physics, Section A. - : Elsevier BV. - 0375-9474. ; 757:1-2, s. 184-283
-
Research review (peer-reviewed)abstract
- Extensive experimental data from high-energy nucleus-nucleus collisions were recorded using the PHENIX detector at the Relativistic Heavy Ion Collider (RHIC). The comprehensive set of measurements from the first three years of RHIC operation includes charged particle multiplicities, transverse energy, yield ratios and spectra of identified hadrons in a wide range of transverse momenta (PT), elliptic flow, two-particle correlations, nonstatistical fluctuations, and suppression of particle production at high PT. The results are examined with an emphasis on implications for the formation of a new state of dense matter. We find that the state of matter created at RHIC cannot be described in terms of ordinary color neutral hadrons.
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| 21. |
- Adler, SS, et al.
(author)
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Improved measurement of double helicity asymmetry in inclulsive midrapidity pi(0) production for polarized p+p collisions at root s=200 GeV
- 2006
-
In: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368. ; 73:9
-
Journal article (peer-reviewed)abstract
- We present an improved measurement of the double helicity asymmetry for pi(0) production in polarized proton-proton scattering at root s=200 GeV employing the PHENIX detector at the Relativistic Heavy Ion Collider (RHIC). The improvements to our previous measurement come from two main factors: Inclusion of a new data set from the 2004 RHIC run with higher beam polarizations than the earlier run and a recalibration of the beam polarization measurements for the earlier run, which resulted in reduced uncertainties and increased beam polarizations. The results are compared to a Next to Leading Order (NLO) perturbative Quantum Chromodynamics (pQCD) calculation with a range of polarized gluon distributions.
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| 22. |
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| 23. |
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| 24. |
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| 25. |
- Clark, Andrew G., et al.
(author)
-
Evolution of genes and genomes on the Drosophila phylogeny
- 2007
-
In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
-
Journal article (peer-reviewed)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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| 26. |
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| 27. |
- Birney, Ewan, et al.
(author)
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
-
In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
-
Journal article (peer-reviewed)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 28. |
- Blackshear, Alice, et al.
(author)
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Intracerebroventricular administration of galanin or galanin receptor subtype 1 agonist M617 induces c-Fos activation in central amygdala and dorsomedial hypothalamus
- 2007
-
In: Peptides. - : Elsevier BV. - 0196-9781 .- 1873-5169. ; 28:5, s. 1120-1124
-
Journal article (peer-reviewed)abstract
- The neuropeptide galanin and galanin receptors are widespread throughout cortical, limbic and midbrain areas implicated in reward, learning/memory, pain, drinking and feeding. While many studies have shown that galanin produces a variety of presynaptic and postsynaptic responses, work studying the effects of galanin on neural activation is limited. The present study examined patterns of c-Fos immunoreactivity resulting from intracerebro-ventricular administration of galanin versus saline injection in awake rats. An initial comprehensive qualitative survey was conducted to identify regions of high c-Fos expression followed up with quantitative analysis. Galanin induced a significant increase in c-Fos levels relative to saline-treated controls in dorsomedial hypothalamus and in the central nucleus of the amygdala. This pattern of activation was also produced by galanin receptor type 1 agonist M617. The present findings confirm that galanin upregulates c-Fos activation in hypothalamic nuclei, and supports roles for galanin in central amygdala-mediated food intake, and Pavlovian conditioning.
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| 29. |
- Margulies, Elliott H, et al.
(author)
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Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
- 2007
-
In: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 17:6, s. 760-774
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Journal article (peer-reviewed)abstract
- A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation, alignment, and evolutionary constraint analyses of 23 mammalian species for all ENCODE targets. Alignments were generated using four different methods; comparisons of these methods reveal large-scale consistency but substantial differences in terms of small genomic rearrangements, sensitivity (sequence coverage), and specificity (alignment accuracy). We describe the quantitative and qualitative trade-offs concomitant with alignment method choice and the levels of technical error that need to be accounted for in applications that require multisequence alignments. Using the generated alignments, we identified constrained regions using three different methods. While the different constraint-detecting methods are in general agreement, there are important discrepancies relating to both the underlying alignments and the specific algorithms. However, by integrating the results across the alignments and constraint-detecting methods, we produced constraint annotations that were found to be robust based on multiple independent measures. Analyses of these annotations illustrate that most classes of experimentally annotated functional elements are enriched for constrained sequences; however, large portions of each class (with the exception of protein-coding sequences) do not overlap constrained regions. The latter elements might not be under primary sequence constraint, might not be constrained across all mammals, or might have expendable molecular functions. Conversely, 40% of the constrained sequences do not overlap any of the functional elements that have been experimentally identified. Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization.
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