| 1. |
- Adare, A., et al.
(författare)
-
Photon-hadron jet correlations in p plus p and Au plus Au collisions at s(NN)=200 GeV
- 2009
-
Ingår i: Physical Review C (Nuclear Physics). - 0556-2813. ; 80:2
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 2. |
- Adare, A., et al.
(författare)
-
Charged hadron multiplicity fluctuations in Au plus Au and Cu plus Cu collisions from s(NN)=22.5 to 200 GeV
- 2008
-
Ingår i: Physical Review C (Nuclear Physics). - 0556-2813. ; 78:4
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 3. |
- Adare, A., et al.
(författare)
-
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
-
Ingår i: Physical Review Letters. - 1079-7114. ; 98:23
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 4. |
- Adare, A., et al.
(författare)
-
Correlated production of p and (p)over-bar in Au+Au collisions at root s(NN)=200 GeV
- 2007
-
Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 649:5-6, s. 359-369
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 5. |
- Adare, A., et al.
(författare)
-
Dihadron azimuthal correlations in Au+Au collisions at root s(NN)=200 GeV
- 2008
-
Ingår i: Physical Review C (Nuclear Physics). - 0556-2813. ; 78:1
-
Tidskriftsartikel (refereegranskat)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).
|
|
| 6. |
- Adare, A., et al.
(författare)
-
J/psi production versus centrality, transverse momentum, and rapidity in Au+Au collisions at root S(NN) = 200 GeV
- 2007
-
Ingår i: Physical Review Letters. - 1079-7114. ; 98:23
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 7. |
- Adare, A., et al.
(författare)
-
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
-
Ingår i: Physical Review C (Nuclear Physics). - 0556-2813. ; 77:6
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 8. |
|
|
| 9. |
- Adare, A., et al.
(författare)
-
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
-
Ingår i: Physical Review C (Nuclear Physics). - 0556-2813. ; 77:1, s. 6-011901
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 10. |
|
|
| 11. |
- Abate, E., et al.
(författare)
-
Combined performance tests before installation of the ATLAS Semiconductor and Transition Radiation Tracking Detectors
- 2008
-
Ingår i: Journal of Instrumentation. - 1748-0221. ; 3
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 12. |
- Adare, A., et al.
(författare)
-
Energy loss and flow of heavy quarks in Au+Au collisions at root s(NN) = 200 GeV
- 2007
-
Ingår i: Physical Review Letters. - 1079-7114. ; 98:17
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 13. |
- Adare, A., et al.
(författare)
-
Scaling properties of azimuthal anisotropy in Au plus Au and Cu plus Cu collisions at root s(NN)=200 GeV
- 2007
-
Ingår i: Physical Review Letters. - 1079-7114. ; 98:16
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 14. |
- Afanasiev, S., et al.
(författare)
-
Charged Kaon Interferometric Probes of Space-Time Evolution in Au plus Au Collisions at s(NN)=200 GeV
- 2009
-
Ingår i: Physical Review Letters. - 1079-7114. ; 103:14
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 15. |
- Afanasiev, S., et al.
(författare)
-
High-p(T) pi(0) production with respect to the reaction plane in Au plus Au collisions at s(NN)=200 GeV
- 2009
-
Ingår i: Physical Review C (Nuclear Physics). - 0556-2813. ; 80:5
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 16. |
- Afanasiev, S., et al.
(författare)
-
Particle-species dependent modification of jet-induced correlations in Au plus Au collisions at root s(NN)=200 GeV
- 2008
-
Ingår i: Physical Review Letters. - 1079-7114. ; 101:8
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 17. |
- Afanasiev, S., et al.
(författare)
-
Photoproduction of J/psi and of high mass e(+)e(-) in ultra-peripheral Au plus Au collisions at root s(NN)=200 GeV
- 2009
-
Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 679:4, s. 321-329
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 18. |
- Afanasiev, S., et al.
(författare)
-
Source breakup dynamics in Au+Au collisions at root s(NN)=200 GeV via three-dimensional two-pion source imaging
- 2008
-
Ingår i: Physical Review Letters. - 1079-7114. ; 100:23
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 19. |
- Afanasiev, S., et al.
(författare)
-
Systematic studies of elliptic flow measurements in Au plus Au collisions at s(NN)=200 GeV
- 2009
-
Ingår i: Physical Review C (Nuclear Physics). - 0556-2813. ; 80:2
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 20. |
- Afanasiev, S., et al.
(författare)
-
Elliptic flow for phi mesons and (Anti)deuterons in Au+Au collisions at root s(NN)=200 GeV
- 2007
-
Ingår i: Physical Review Letters. - 1079-7114. ; 99:5
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 21. |
- Adcox, K, et al.
(författare)
-
Formation of dense partonic matter in relativistic nucleus-nucleus collisions at RHIC: Experimental evaluation by the PHENIX Collaboration
- 2005
-
Ingår i: Nuclear Physics, Section A. - : Elsevier BV. - 0375-9474. ; 757:1-2, s. 184-283
-
Forskningsöversikt (refereegranskat)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.
|
|
| 22. |
- Adler, SS, et al.
(författare)
-
Improved measurement of double helicity asymmetry in inclulsive midrapidity pi(0) production for polarized p+p collisions at root s=200 GeV
- 2006
-
Ingår i: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368. ; 73:9
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 23. |
- Birney, Ewan, et al.
(författare)
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 24. |
|
|
| 25. |
- Clark, Andrew G., et al.
(författare)
-
Evolution of genes and genomes on the Drosophila phylogeny
- 2007
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 26. |
|
|
| 27. |
|
|
| 28. |
|
|
| 29. |
- Rantalainen, Mattias, et al.
(författare)
-
Statistically Integrated Metabonomic-Proteomic Studies on a Human Prostate Cancer Xenograft Model in Mice
- 2006
-
Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 10, s. 2642-55
-
Tidskriftsartikel (refereegranskat)abstract
- A novel statistically integrated proteometabonomic method has been developed and applied to a human tumor xenograft mouse model of prostate cancer. Parallel 2D-DIGE proteomic and 1H NMR metabolic profile data were collected on blood plasma from mice implanted with a prostate cancer (PC-3) xenograft and from matched control animals. To interpret the xenograft-induced differences in plasma profiles, multivariate statistical algorithms including orthogonal projection to latent structure (OPLS) were applied to generate models characterizing the disease profile. Two approaches to integrating metabonomic data matrices are presented based on OPLS algorithms to provide a framework for generating models relating to the specific and common sources of variation in the metabolite concentrations and protein abundances that can be directly related to the disease model. Multiple correlations between metabolites and proteins were found, including associations between serotransferrin precursor and both tyrosine and 3-D-hydroxybutyrate. Additionally, a correlation between decreased concentration of tyrosine and increased presence of gelsolin was also observed. This approach can provide enhanced recovery of combination candidate biomarkers across multi-omic platforms, thus, enhancing understanding of in vivo model systems studied by multiple omic technologies
|
|
| 30. |
- Andzane, Jana, et al.
(författare)
-
Selection of Application Specific Single and Multi Walled Carbon Nanotubes by In Situ Characterization of Conductive and Field Emission Properties
- 2007
-
Ingår i: AZojono - Journal of Nanotechnology online.
-
Tidskriftsartikel (refereegranskat)abstract
- The conductive and field emission properties of individual single and multi-walled carbon nanotubes, grown by chemical vapour and supercritical fluid deposition techniques, have been assessed using an in-situ transmission electron microscope-scanning tunnelling microscope (TEM-STM) technique. The conductivity and field emission measurements were obtained from nanotube-electrode distance and contact observations. Experimental field emission characteristics for all carbon nanotubes investigated fitted well to the Fowler-Nordheim equation when different work functions were applied. Differences in field emission and conductive properties are analysed and related to the structure of the carbon nanotubes. The method presented here is suitable for in situ selection of CNT with desired properties for particular electronic applications.
|
|
| 31. |
|
|
| 32. |
- Bollard, Mary E, et al.
(författare)
-
Comparative metabonomics of differential hydrazine toxicity in the rat and mouse
- 2005
-
Ingår i: Toxicology and Applied Pharmacology. - : Elsevier BV. - 0041-008X. ; 204:2, s. 135-51
-
Tidskriftsartikel (refereegranskat)abstract
- Interspecies variation between rats and mice has been studied for hydrazine toxicity using a novel metabonomics approach. Hydrazine hydrochloride was administered to male Sprague–Dawley rats (30 mg/kg, n = 10 and 90 mg/kg, n = 10) and male B6C3F mice (100 mg/kg, n = 8 and 250 mg/kg, n = 8) by oral gavage. In each species, the high dose was selected to produce the major histopathologic effect, hepatocellular lipid accumulation. Urine samples were collected at sequential time points up to 168 h post dose and analyzed by 1H NMR spectroscopy. The metabolites of hydrazine, namely diacetyl hydrazine and 1,4,5,6-tetrahydro-6-oxo-3-pyridazine carboxylic acid (THOPC), were detected in both the rat and mouse urine samples. Monoacetyl hydrazine was detected only in urine samples from the rat and its absence in the urine of the mouse was attributed to a higher activity of N-acetyl transferases in the mouse compared with the rat. Differential metabolic effects observed between the two species included elevated urinary β-alanine, 3-d-hydroxybutyrate, citrulline, N-acetylcitrulline, and reduced trimethylamine-N-oxide excretion unique to the rat. Metabolic principal component (PC) trajectories highlighted the greater degree of toxic response in the rat. A data scaling method, scaled to maximum aligned and reduced trajectories (SMART) analysis, was used to remove the differences between the metabolic starting positions of the rat and mouse and varying magnitudes of effect, to facilitate comparison of the response geometries between the rat and mouse. Mice followed “biphasic” open PC trajectories, with incomplete recovery 7 days after dosing, whereas rats followed closed “hairpin” time profiles, indicating functional reversibility. The greater magnitude of metabolic effects observed in the rat was supported by the more pronounced effect on liver pathology in the rat when compared with the mouse.
|
|
| 33. |
- Holmes, Emily A., et al.
(författare)
-
Are there two qualitatively distinct forms of dissociation? : A review and some clinical implications
- 2005
-
Ingår i: Clinical Psychology Review. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0272-7358 .- 1873-7811. ; 25:1, s. 1-23
-
Forskningsöversikt (refereegranskat)abstract
- This review aims to clarify the use of the term 'dissociation' in theory, research and clinical practice. Current psychiatric definitions of dissociation are contrasted with recent conceptualizations that have converged on a dichotomy between two qualitatively different phenomena: 'detachment' and 'compartmentalization'. We review some evidence for this distinction within the domains of phenomenology, factor analysis of self-report scales and experimental research. Available evidence supports the distinction but more controlled evaluations are needed. We conclude with recommendations for future research and clinical practice, proposing that using this dichotomy can lead to clearer case formulation and an improved choice of treatment strategy. Examples are provided within Depersonalization Disorder, Conversation Disorder and Posttraumatic Stress Disorder (PTSD). (C) 2004 Elsevier Ltd. All rights reserved.
|
|
| 34. |
- Holmes, Emily A., et al.
(författare)
-
Intrusive images and "hotspots" of trauma memories in Posttraumatic Stress Disorder : an exploratory investigation of emotions and cognitive themes
- 2005
-
Ingår i: Journal of Behavior Therapy and Experimental Psychiatry. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0005-7916 .- 1873-7943. ; 36:1, s. 3-17
-
Tidskriftsartikel (refereegranskat)abstract
- This study aimed to investigate the emotions and cognitions contained in "hotspots" of memory for trauma, as well as their associated images. Thirty-two participants at a specialist outpatient trauma clinic had experienced a range of traumatic events and met diagnostic criteria for Posttraumatic Stress Disorder (PTSD). Data were collected within an agreed protocol, involving reliving therapy. Patients described the different intrusive images of the trauma that they were re-experiencing. Their reports of cognitions and emotions during "hotspots" in their memory of the traumatic experience were recorded as part of reliving therapy. Hotspots refer to moments of peak emotional distress during the event. There was a high degree of match reported between intrusive images and hotspots. The cognitive and emotional contents of hotspots were qualitatively analysed into themes. The relative of frequency of these peritraumatic themes is presented. The exploratory findings are discussed with respect to our understanding and treatment of intrusive imagery in PTSD. (C) 2004 Elsevier Ltd. All rights reserved.
|
|
| 35. |
- Holmes, Emily A., et al.
(författare)
-
Investigating peri-traumatic dissociation using hypnosis during a traumatic film.
- 2006
-
Ingår i: Journal of Trauma & Dissociation. - 1529-9732 .- 1529-9740. ; 7:4, s. 91-113
-
Tidskriftsartikel (refereegranskat)abstract
- We investigated the hypothesis that inducing a dissociative response (detachment) in healthy volunteers while they were watching a trauma film would lead to increased numbers of intrusive memories of the film during the following week. Hypnotized participants were given suggestions to dissociate during part of the film, and to watch the rest of the film normally from their own perspective. The order of these conditions, and the section of film watched under the two conditions, were counterbalanced. As predicted, watching the film under both conditions led to increases in dissociation. Explicit suggestions to dissociate were generally effective in inducing higher levels of dissociation. Contrary to prediction, there were no more intrusive memories of sections of the film for which participants had received dissociation suggestions. Implications of our results for views of the relationship between peri-traumatic dissociation and intrusive memories are discussed.
|
|
| 36. |
- Margulies, Elliott H, et al.
(författare)
-
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
- 2007
-
Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 17:6, s. 760-774
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 37. |
- Mirone, V, et al.
(författare)
-
An evaluation of an alternative dosing regimen with tadalafil, 3 times/week, for men with erectile dysfunction: SURE study in 14 European countries.
- 2005
-
Ingår i: Eur Urol. - : Elsevier BV. ; 47:6, s. 846-854
-
Tidskriftsartikel (refereegranskat)abstract
- Objective: To examine the preference for 2 dosing regimens (on demand or 3 times/week) for tadalafil, a phosphodiesterase 5 inhibitor with a duration of effectiveness up to 36 hours in men with erectile dysfunction (ED). Design and methods: SURE is a 14 European country, multicenter, crossover, and open-label study. Men with ED (N = 4262) were randomized to tadalafil 20 mg treatment on demand (maximum one dose per day and before sexual activity) or 3 times/week for 5–6 weeks. After a 1-week washout period, patients were crossed over to the alternate regimen for 5–6 weeks. The patient's response to a treatment preference question (TPQ) was used to determine the preferred treatment regimen. Results: The mean age of the randomized patients was 55 years and 85.2% reported a history of ED for one year or greater. Overall, the responses of 3861 men to the TPQ assessment showed that 57.8% preferred the on-demand regimen and 42.2% preferred the 3 times/week dosing. Both regimens were efficacious and well tolerated. Conclusions: In this study, while 57.8% of men preferred the on-demand regimen of tadalafil 20 mg, a substantial number (42.2%) preferred the 3 times/week treatment. The two regimens provide additional treatment options by giving men with erectile dysfunction unique flexibility in dosing with tadalafil.
|
|
| 38. |
- Nene, Vishvanath, et al.
(författare)
-
Genome sequence of Aedes aegypti, a major arbovirus vector.
- 2007
-
Ingår i: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 316:5832, s. 1718-23
-
Tidskriftsartikel (refereegranskat)abstract
- We present a draft sequence of the genome of Aedes aegypti, the primary vector for yellow fever and dengue fever, which at approximately 1376 million base pairs is about 5 times the size of the genome of the malaria vector Anopheles gambiae. Nearly 50% of the Ae. aegypti genome consists of transposable elements. These contribute to a factor of approximately 4 to 6 increase in average gene length and in sizes of intergenic regions relative to An. gambiae and Drosophila melanogaster. Nonetheless, chromosomal synteny is generally maintained among all three insects, although conservation of orthologous gene order is higher (by a factor of approximately 2) between the mosquito species than between either of them and the fruit fly. An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species.
|
|
| 39. |
- O'Byrne, Justin P., et al.
(författare)
-
Novel catalysts for carbon nanotube and nanofibre synthesis
- 2009
-
Konferensbidrag (refereegranskat)abstract
- Carbon nanotubes are of huge interest to the scientific community for their physical and electronic properties[1]. We have synthesized carbon nanotubes (CNTs) on novel non-traditonal catalysts. Bamboo-shaped carbon nanotubes (BCNTs) were synthesized on Pd and Cu catalysts doped with either Mo or W. BCNTs were sythesised using the catalytic chemical vapour decomposition (CVD) of methane. Cu is catalytically inactive for the synthesis of CNTs; however this is not the case when Cu is doped with Mo[2] and W. When Cu is doped with these metals bamboo structured CNTs can be produced via a CVD synthesis method. The addition of a dopant alters the electronic structure of catalyst nanoparticle causing the binding strength between the nanoparticle and carbon to approach that of traditional catalysts for CNT growth i.e. Fe; Co; Ni and their alloys which has been shown by computer modeling. We have performed full geometry optimization DFT calculations of Cu/W and Pd/Mo particles of different compositions to determine their ability to stabilize and support the growing end of a CNT. We have computed a (5;0) SWNTs binding energy to a M13 metal cluster (M=Cu; W or Pd; Mo); which in a model system that has been proven to correctly predict the trends in bonding[2; 3]. The resulting binding energies are compared to Fe; Co; Ni and Cu/Mo clusters of these previous reports. All calculations were made using the generalized gradient approximation (GGA) exchange and correlation potential by Perdew-Burke-Ernzenhof [PBE]; utilizing the polarized valence triple-ζ (TZVP) basis set[4] and relativistic effective core potentials (ECPs) for Cu; Pd; W and Mo[5; 6]; as implemented in the Turbomole suite of programs[7-10].
|
|
| 40. |
- Rantalainen, Mattias, et al.
(författare)
-
Piecewise multivariate modelling of sequential metabolic profiling data
- 2008
-
Ingår i: BMC Bioinformatics. - : EMBO. - 1471-2105. ; 9, s. 105-
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Modelling the time-related behaviour of biological systems is essential for understanding their dynamic responses to perturbations. In metabolic profiling studies, the sampling rate and number of sampling points are often restricted due to experimental and biological constraints. Results: A supervised multivariate modelling approach with the objective to model the time-related variation in the data for short and sparsely sampled time-series is described. A set of piecewise Orthogonal Projections to Latent Structures (OPLS) models are estimated, describing changes between successive time points. The individual OPLS models are linear, but the piecewise combination of several models accommodates modelling and prediction of changes which are non-linear with respect to the time course. We demonstrate the method on both simulated and metabolic profiling data, illustrating how time related changes are successfully modelled and predicted. Conclusion: The proposed method is effective for modelling and prediction of short and multivariate time series data. A key advantage of the method is model transparency, allowing easy interpretation of time-related variation in the data. The method provides a competitive complement to commonly applied multivariate methods such as OPLS and Principal Component Analysis (PCA) for modelling and analysis of short time-series data.
|
|
| 41. |
- Raune, D, et al.
(författare)
-
The simulation heuristic and visual imagery in pessimism for future negative events in anxiety
- 2005
-
Ingår i: Clinical Psychology and Psychotherapy. - : JOHN WILEY & SONS LTD. - 1063-3995 .- 1099-0879. ; 12:4, s. 313-325
-
Tidskriftsartikel (refereegranskat)abstract
- A salient feature of clinical anxiety and its disorders is an elevated subjective probability judgement that future negative events will happen to the individual. A neglected area of research is the cognitive mechanisms that might underlie this judgement in patient populations. First, we investigated the ease of being able to simulate imaginary negative events happening to the individual ('the simulation heuristic'). Second, we conducted the first investigation to our knowledge into the possible role of visual imagery characteristics on subjective probability for negative events. Twenty-six patients who had a clinical level of anxiety and 26 low-anxiety control participants simulated mentally and also formed visual images of future negative events. They then rated the likelihood of the events happening to them. As predicted, with anxious patients the simulation heuristic was correlated with subjective probability, and they reported increased access to their simulations compared to control participants. The visual image results were more complex: anxious patients' ease of image formation was correlated with subjective probability but did not differ from that of the control participants, and vividness and dismissibility were enhanced in anxious patients but did not correlate with subjective probability. Clinically, helping anxious patients to improve their access to simulations of why events will not happen may help lower their subjective probability. Future research could seek to confirm this experimentally in a clinical intervention study, as well as isolate further the different roles particular visual image characteristics may play in specific aspects of clinical anxiety. Copyright (c) 2005 John Wiley & Sons, Ltd.
|
|
| 42. |
|
|
| 43. |
|
|
| 44. |
- Serruys, Patrick W., et al.
(författare)
-
Percutaneous coronary intervention versus coronary-artery bypass grafting for severe coronary artery disease
- 2009
-
Ingår i: New England Journal of Medicine. - 0028-4793 .- 1533-4406. ; 360:10, s. 961-972
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Percutaneous coronary intervention (PCI) involving drug-eluting stents is increasingly used to treat complex coronary artery disease, although coronary-artery bypass grafting (CABG) has been the treatment of choice historically. Our trial compared PCI and CABG for treating patients with previously untreated three-vessel or left main coronary artery disease (or both). METHODS: We randomly assigned 1800 patients with three-vessel or left main coronary artery disease to undergo CABG or PCI (in a 1:1 ratio). For all these patients, the local cardiac surgeon and interventional cardiologist determined that equivalent anatomical revascularization could be achieved with either treatment. A noninferiority comparison of the two groups was performed for the primary end point--a major adverse cardiac or cerebrovascular event (i.e., death from any cause, stroke, myocardial infarction, or repeat revascularization) during the 12-month period after randomization. Patients for whom only one of the two treatment options would be beneficial, because of anatomical features or clinical conditions, were entered into a parallel, nested CABG or PCI registry. RESULTS: Most of the preoperative characteristics were similar in the two groups. Rates of major adverse cardiac or cerebrovascular events at 12 months were significantly higher in the PCI group (17.8%, vs. 12.4% for CABG; P=0.002), in large part because of an increased rate of repeat revascularization (13.5% vs. 5.9%, P<0.001); as a result, the criterion for noninferiority was not met. At 12 months, the rates of death and myocardial infarction were similar between the two groups; stroke was significantly more likely to occur with CABG (2.2%, vs. 0.6% with PCI; P=0.003). CONCLUSIONS: CABG remains the standard of care for patients with three-vessel or left main coronary artery disease, since the use of CABG, as compared with PCI, resulted in lower rates of the combined end point of major adverse cardiac or cerebrovascular events at 1 year. (ClinicalTrials.gov number, NCT00114972.)
|
|
| 45. |
- Steel, C, et al.
(författare)
-
Trauma-related intrusions and psychosis : An information processing account
- 2005
-
Ingår i: Behavioural and Cognitive Psychotherapy. - : CAMBRIDGE UNIV PRESS. - 1352-4658 .- 1469-1833. ; 33:2, s. 139-152
-
Tidskriftsartikel (refereegranskat)abstract
- There is active, current speculation about the relationship between trauma and psychosis. However, little is known about the information-processing mechanisms underlying the development of trauma-related intrusions in this area. Our account highlights the role of contextual integration, i.e. the need for experiential information to be effectively integrated into a temporal and spatial context in order to facilitate voluntary recall. Drawing on existing models of both posttraumatic stress disorder (PTSD) and psychosis (Brewin, 2001; Ehlers and Clark, 2000; Garety et al., 2001; Morrison, 2001), we propose a contextual integration account of trauma-related intrusions. It is argued that the strength of contextual integration, which occurs during encoding, influences the frequency and nature of subsequent intrusive experiences. Consequently, individual differences in schizotypal personality traits, which are known to be associated with levels of contextual integration, are also related to the phenomenology of trauma-related intrusions. Whilst intrusions can be seen to occur within a range of disorders, it is argued that contextual integration may be one key variable in understanding the relationship between an experienced trauma and any consequent psychiatric symptomatology. Implications for clinical interventions aimed at trauma-related psychosis are discussed, along with research aimed at developing the empirical basis for such interventions.
|
|
| 46. |
- Stuart, A D P, et al.
(författare)
-
The influence of a visuospatial grounding task on intrusive images of a traumatic film
- 2006
-
Ingår i: Behaviour Research and Therapy. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0005-7967 .- 1873-622X. ; 44:4, s. 611-619
-
Tidskriftsartikel (refereegranskat)abstract
- Nonclinical participants watched a trauma film under two processing conditions. During part of the film participants carried out a concurrent visuospatial grounding task consisting of the construction of shapes out of plasticine (modelling clay), while the rest of the film constituted a control, no task condition. The visuospatial task was predicted to selectively compete for processing resources required for intrusive image formation. As predicted, spontaneous intrusive images during the succeeding week were significantly less common from those parts of the film that coincided with the concurrent task. The task had no effect on levels of distress or peritraumatic dissociation, consistent with the hypothesis that intrusions were reduced because the task competed for resources necessary for encoding into an image-based memory system. (c) 2005 Elsevier Ltd. All rights reserved.
|
|
| 47. |
|
|
| 48. |
|
|
| 49. |
- Zhonglai, Li, et al.
(författare)
-
Copper/Molybdenum Nanocomposite Particles as Catalysts for the Growth of Bamboo-Structured Carbon Nanotubes
- 2008
-
Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 112:32, s. 12201-12206
-
Tidskriftsartikel (refereegranskat)abstract
- Bamboo-structured carbon nanotubes (BCNTs), with mean diameters of 20 nm, have been synthesized on MgO-supported Cu and Mo catalysts by the catalytic chemical vapor deposition of methane. BCNTs could only be generated using a combination of Cu and Mo catalysts. No BCNTs were produced from either individual Cu or Mo catalysts. In combination, Mo was found to be essential for cracking the methane precursor, while Cu was required for BCNT formation. Energy dispersive X-ray analysis of the individual particles at the tips of the nanotubes suggest that Cu and Mo are present as a “composite” nanoparticle catalyst after growth. First-principles modeling has been used to describe the interaction of the Cu/Mo catalyst with the nanotubes, suggesting that the catalyst binds with the same energy as traditional catalysts such as Fe, Ni, and Co.
|
|
