| 1. |
- Adare, A., et al.
(författare)
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Photon-hadron jet correlations in p plus p and Au plus Au collisions at s(NN)=200 GeV
- 2009
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Ingår i: Physical Review C (Nuclear Physics). - 0556-2813. ; 80:2
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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.
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| 2. |
- Adare, A., et al.
(författare)
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Measurement of Bottom Versus Charm as a Function of Transverse Momentum with Electron-Hadron Correlations in p plus p Collisions at s=200 GeV
- 2009
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Ingår i: Physical Review Letters. - 1079-7114. ; 103:8
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Tidskriftsartikel (refereegranskat)abstract
- The momentum distribution of electrons from semileptonic decays of charm and bottom quarks for midrapidity |y|< 0.35 in p+p collisions at s=200 GeV is measured by the PHENIX experiment at the Relativistic Heavy Ion Collider over the transverse momentum range 2 < p(T)< 7 GeV/c. The ratio of the yield of electrons from bottom to that from charm is presented. The ratio is determined using partial D/D -> e(+/-)K(-/+)X (K unidentified) reconstruction. It is found that the yield of electrons from bottom becomes significant above 4 GeV/c in p(T). A fixed-order-plus-next-to-leading-log perturbative quantum chromodynamics calculation agrees with the data within the theoretical and experimental uncertainties. The extracted total bottom production cross section at this energy is sigma(bb)=3.2(-1.1)(+1.2)(stat)(-1.3)(+1.4)(syst)mu b.
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| 3. |
- Adare, A., et al.
(författare)
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Onset of pi(0) Suppression Studied in Cu plus Cu Collisions at root s(NN)=22.4, 62.4, and 200 GeV
- 2008
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Ingår i: Physical Review Letters. - 1079-7114. ; 101:16
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Tidskriftsartikel (refereegranskat)abstract
- Neutral pion transverse momentum (p(T)) spectra at midrapidity (|y| less than or similar to 0.35) were measured in Cu + Cu collisions at root s(NN) = 22.4, 62.4, and 200 GeV. Relative to pi(0) yields in p + p collisions scaled by the number of inelastic nucleon-nucleon collisions (N-coll) the pi(0) yields for p(T) greater than or similar to 2 GeV/c in central Cu + Cu collisions are suppressed at 62.4 and 200 GeV whereas an enhancement is observed at 22.4 GeV. A comparison with a jet-quenching model suggests that final state parton energy loss dominates in central Cu + Cu collisions at 62.4 and 200 GeV, while the enhancement at 22.4 GeV is consistent with nuclear modifications in the initial state alone.
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| 4. |
- Adare, A., et al.
(författare)
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Gluon-Spin Contribution to the Proton Spin from the Double-Helicity Asymmetry in Inclusive pi(0) Production in Polarized p plus p Collisions at root s=200 GeV
- 2009
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Ingår i: Physical Review Letters. - 1079-7114. ; 103:1
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Tidskriftsartikel (refereegranskat)abstract
- The double helicity asymmetry in neutral pion production for p(T) = 1 to 12 GeV/c was measured with the PHENIX experiment to access the gluon-spin contribution, Delta G, to the proton spin. Measured asymmetries are consistent with zero, and at a theory scale of mu 2 = 4 GeV2 a next to leading order QCD analysis gives Delta G([0.02,0.3]) = 0.2, with a constraint of -0.7 < Delta G([0.02,0.3]) < 0.5 at Delta chi(2) = 9 (similar to 3 sigma) for the sampled gluon momentum fraction (x) range, 0.02 to 0.3. The results are obtained using predictions for the measured asymmetries generated from four representative fits to polarized deep inelastic scattering data. We also consider the dependence of the Delta G constraint on the choice of the theoretical scale, a dominant uncertainty in these predictions.
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| 5. |
- Adare, A., et al.
(författare)
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Inclusive cross section and double helicity asymmetry for pi(0) production in p plus p collisions at root s=62.4 GeV
- 2009
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Ingår i: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368. ; 79:1
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Tidskriftsartikel (refereegranskat)abstract
- The PHENIX experiment presents results from the RHIC 2006 run with polarized p + p collisions at root s = 62.4 GeV, for inclusive pi(0) production at midrapidity. Unpolarized cross section results are measured for transverse momenta p(T) = 0.5 to 7 GeV/c. Next-to-leading order perturbative quantum chromodynamics calculations are compared with the data, and while the calculations are consistent with the measurements, next-to-leading logarithmic corrections improve the agreement. Double helicity asymmetries A(LL) are presented for p(T) = 1 to 4 GeV/c and probe the higher range of Bjorken x of the gluon (x(g)) with better statistical precision than our previous measurements at root s = 200 GeV. These measurements are sensitive to the gluon polarization in the proton for 0.06 < x(g) < 0.4.
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| 6. |
- Ablikim, M., et al.
(författare)
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Measurements of (XcJ)-> K+K-K+K- decays
- 2006
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Ingår i: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 642:3, s. 197-202
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Tidskriftsartikel (refereegranskat)abstract
- Using 14M psi(2S) events taken with the BESII detector, chi(cJ) -> 2(K+K-) decays are studied. For the four-kaon final state, the branching fractions are B(chi(c0,1,2) ->.2(K+K-)) = (3.48 +/- 0.23 +/- 0.47) x 10(-3), (0.70 +/- 0.13 +/- 0.10) x 10(-3), and (2.17 +/- 0.20 +/- 0.31) x 10(-3). For the phi K+K- final state, the branching fractions, which are measured for the first time, are B(chi(c0,1,2) -> phi K+K-) = (1.03 +/- 0.22 +/- 0.15) x 10(-3), (0.46 +/- 0.16 +/- 0.06) x 10(-3), and (1.67 +/- 0.26 +/- 0.24) x 10(-4). For the phi phi final state, B(chi(c0,2) -> phi phi) = (0.94 +/- 0.21 +/- 0.13) x 10(-3) and (1.70 +/- 0.30 +/- 0.25) x 10(-3).
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| 7. |
- Clark, Andrew G., et al.
(författare)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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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.
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| 8. |
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| 9. |
- Birney, Ewan, et al.
(författare)
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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
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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.
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| 10. |
- Carninci, P, et al.
(författare)
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The transcriptional landscape of the mammalian genome
- 2005
-
Ingår i: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 309:5740, s. 1559-1563
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Tidskriftsartikel (refereegranskat)abstract
- This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5′ and 3′ boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.
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| 11. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
- 2008
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Ingår i: Autophagy. - : Landes Bioscience. - 1554-8627 .- 1554-8635. ; 4:2, s. 151-175
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Forskningsöversikt (refereegranskat)abstract
- Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.
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| 12. |
- Harley, John B., et al.
(författare)
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Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci
- 2008
-
Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 40:2, s. 204-10
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Tidskriftsartikel (refereegranskat)abstract
- Systemic lupus erythematosus (SLE) is a common systemic autoimmune disease with complex etiology but strong clustering in families (lambda(S) = approximately 30). We performed a genome-wide association scan using 317,501 SNPs in 720 women of European ancestry with SLE and in 2,337 controls, and we genotyped consistently associated SNPs in two additional independent sample sets totaling 1,846 affected women and 1,825 controls. Aside from the expected strong association between SLE and the HLA region on chromosome 6p21 and the previously confirmed non-HLA locus IRF5 on chromosome 7q32, we found evidence of association with replication (1.1 x 10(-7) < P(overall) < 1.6 x 10(-23); odds ratio = 0.82-1.62) in four regions: 16p11.2 (ITGAM), 11p15.5 (KIAA1542), 3p14.3 (PXK) and 1q25.1 (rs10798269). We also found evidence for association (P < 1 x 10(-5)) at FCGR2A, PTPN22 and STAT4, regions previously associated with SLE and other autoimmune diseases, as well as at > or =9 other loci (P < 2 x 10(-7)). Our results show that numerous genes, some with known immune-related functions, predispose to SLE.
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| 13. |
- Amundadottir, Laufey, et al.
(författare)
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Genome-wide association study identifies variants in the ABO locus associated with susceptibility to pancreatic cancer.
- 2009
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 41, s. 986-990
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Tidskriftsartikel (refereegranskat)abstract
- We conducted a two-stage genome-wide association study of pancreatic cancer, a cancer with one of the lowest survival rates worldwide. We genotyped 558,542 SNPs in 1,896 individuals with pancreatic cancer and 1,939 controls drawn from 12 prospective cohorts plus one hospital-based case-control study. We conducted a combined analysis of these groups plus an additional 2,457 affected individuals and 2,654 controls from eight case-control studies, adjusting for study, sex, ancestry and five principal components. We identified an association between a locus on 9q34 and pancreatic cancer marked by the SNP rs505922 (combined P = 5.37 x 10(-8); multiplicative per-allele odds ratio 1.20; 95% confidence interval 1.12-1.28). This SNP maps to the first intron of the ABO blood group gene. Our results are consistent with earlier epidemiologic evidence suggesting that people with blood group O may have a lower risk of pancreatic cancer than those with groups A or B.
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| 14. |
- Armstrong, Paul W., et al.
(författare)
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Efficacy and safety of unfractionated heparin versus enoxaparin : a pooled analysis of ASSENT-3 and -3 PLUS data
- 2006
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Ingår i: CMJA. Canadian Medical Association Journal. Onlineutg. Med tittel. - : CMA Joule Inc.. - 0820-3946 .- 1488-2329. ; 174:10, s. 1421-1426
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The optimal antithrombotic therapy to accompany tenecteplase in cases of acute ST-segment elevation myocardial infarction (STEMI) remains unclear. We undertook a prespecified pooled analysis of data from the ASSENT-3 and ASSENT-3 PLUS trials. METHODS: We created a combined database of the 2040 and 818 patients who received enoxaparin in ASSENT-3 and ASSENT-3 PLUS, respectively, and compared them with the 2038 and 821 patients who received unfractionated heparin. RESULTS: The efficacy end point (a composite of 30-day mortality, reinfarction or refractory ischemia) was 12.2% with enoxaparin versus 16.0% with unfractionated heparin (p < 0.001); the combined end point of efficacy plus safety (a composite of 30-day mortality, reinfarction, refractory ischemia, intracranial hemorrhage [ICH] or major systemic bleeding) was 15.0% versus 18.0%, respectively (p = 0.003) [corrected] The 1049 patients urgently revascularized had greater benefit from enoxaparin (15.4% v. 10.1%, p = 0.013), yet the excess in major systemic bleeding evident with enoxaparin (3.3% v. 2.4%, p = 0.01) was largely confined to the 3492 patients without or before revascularization. Although ICH rates in the groups were similar (1.3% v. 0.9%, p = 0.26), an excess of ICH occurred among those administered enoxaparin during the ASSENT-3 PLUS trial (6.7% v. 0.8%, p = 0.013), especially among women over 75 years of age. INTERPRETATION: These data demonstrated the benefit of enoxaparin used in conjunction with tenecteplase, but raised caution about its prehospital use to treat STEMI in elderly women.
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| 15. |
- Aucott, Rebecca, et al.
(författare)
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HP1-beta is required for development of the cerebral neocortex and neuromuscular junctions
- 2008
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Ingår i: Journal of Cell Biology. - : Rockefeller University Press. - 0021-9525 .- 1540-8140. ; 183:4, s. 597-606
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Tidskriftsartikel (refereegranskat)abstract
- HP1 proteins are thought to be modulators of chromatin organization in all mammals, yet their exact physiological function remains unknown. In a first attempt to elucidate the function of these proteins in vivo, we disrupted the murine Cbx1 gene, which encodes the HP1-beta isotype, and show that the Cbx1(-/-) null mutation leads to perinatal lethality. The newborn mice succumbed to acute respiratory failure, whose likely cause is the defective development of neuromuscular junctions within the endplate of the diaphragm. We also observe aberrant cerebral cortex development in Cbx1(-/-) mutant brains, which have reduced proliferation of neuronal precursors, widespread cell death, and edema. In vitro cultures of neurospheres from Cbx1(-/-) mutant brains reveal a dramatic genomic instability. Our results demonstrate that HP1 proteins are not functionally redundant and that they are likely to regulate lineage-specific changes in heterochromatin organization.
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| 16. |
- Biro, T, et al.
(författare)
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How best to fight that nasty itch - from new insights into the neuroimmunological, neuroendocrine, and neurophysiological bases of pruritus to novel therapeutic approaches
- 2005
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Ingår i: Experimental Dermatology. - : Wiley. - 0906-6705 .- 1600-0625. ; 14:3, s. 225-225
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Tidskriftsartikel (refereegranskat)abstract
- While the enormous clinical and psychosocial importance of pruritus in many areas of medicine and the detrimental effects of chronic 'itch' on the quality of life of an affected individual are widely appreciated, the complexity of this sensation is still often grossly underestimated. The current Controversies feature highlights this complexity by portraying pruritus as a truly interdisciplinary problem at the crossroads of neurophysiology, neuroimmunology, neuropharmacology, protease research, internal medicine, and dermatology, which is combated most successfully if one keeps the multilayered nature of 'itch' in mind and adopts a holistic treatment approach - beyond the customary, frequently frustrane monotherapy with histamine receptor antagonists. In view of the often unsatisfactory, unidimensional, and altogether rather crude standard instruments for pruritus management that we still tend to use in clinical practice today, an interdisciplinary team of pruritus experts here critically examines recent progress in pruritus research that future itch management must take into consideration. Focusing on new insights into the neuroimmunological, neuroendocrine, and neurophysiological bases of pruritus, and discussing available neuropharmacological tools, specific research avenues are highlighted, whose pursuit promises to lead to novel, and hopefully more effective, forms of pruritus management.
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| 17. |
- Chang, Wei-Ching, et al.
(författare)
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Forecasting mortality : dynamic assessment of risk in ST-segment elevation acute myocardial infarction
- 2006
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Ingår i: European Heart Journal. - : Oxford University Press (OUP). - 0195-668X .- 1522-9645. ; 27:4, s. 419-426
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Tidskriftsartikel (refereegranskat)abstract
- AIMS: To demonstrate the feasibility and clinical utility of developing dynamic risk assessment models for ST-segment elevation myocardial infarction (STEMI) patients. METHODS AND RESULTS: In 6066 STEMI patients enrolled in the Assessment of the Safety and Efficacy of a New Thrombolytic-3 (ASSENT-3) trial with complete electrocardiographic data, we assessed the probability of 30-day mortality over the following forecasting periods beginning at day 0 (baseline), 3 h, day 2, and day 5 using multiple-logistic regression. These models were validated and simplified in independent samples of 1622 similar fibrinolytic-treated patients from the ASSENT-3 PLUS trial and in 814 STEMI patients undergoing primary percutaneous coronary intervention in the COMplement inhibition in Myocardial infarction treated with Angioplasty (COMMA) trial. The discriminatory power of these predictive models, from baseline to day 5, was excellent (c-statistics 0.80 to 0.87); and their predictive ability was supported by strong gradients in mortality outcomes as the risk score increased. Dynamic modelling also provided information on the change in prognosis over time which may be used to advise more appropriate therapeutic decisions, e.g. the identification of high-risk patients for possible co-interventions. CONCLUSION: Dynamic modelling for STEMI patients enhances the risk assessment and stratification and should provide valuable ongoing guidance for their management.
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| 18. |
- Euskirchen, Ghia M, et al.
(författare)
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Mapping of transcription factor binding regions in mammalian cells by ChIP : comparison of array- and sequencing-based technologies.
- 2007
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 17:6, s. 898-909
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Tidskriftsartikel (refereegranskat)abstract
- Recent progress in mapping transcription factor (TF) binding regions can largely be credited to chromatin immunoprecipitation (ChIP) technologies. We compared strategies for mapping TF binding regions in mammalian cells using two different ChIP schemes: ChIP with DNA microarray analysis (ChIP-chip) and ChIP with DNA sequencing (ChIP-PET). We first investigated parameters central to obtaining robust ChIP-chip data sets by analyzing STAT1 targets in the ENCODE regions of the human genome, and then compared ChIP-chip to ChIP-PET. We devised methods for scoring and comparing results among various tiling arrays and examined parameters such as DNA microarray format, oligonucleotide length, hybridization conditions, and the use of competitor Cot-1 DNA. The best performance was achieved with high-density oligonucleotide arrays, oligonucleotides >/=50 bases (b), the presence of competitor Cot-1 DNA and hybridizations conducted in microfluidics stations. When target identification was evaluated as a function of array number, 80%-86% of targets were identified with three or more arrays. Comparison of ChIP-chip with ChIP-PET revealed strong agreement for the highest ranked targets with less overlap for the low ranked targets. With advantages and disadvantages unique to each approach, we found that ChIP-chip and ChIP-PET are frequently complementary in their relative abilities to detect STAT1 targets for the lower ranked targets; each method detected validated targets that were missed by the other method. The most comprehensive list of STAT1 binding regions is obtained by merging results from ChIP-chip and ChIP-sequencing. Overall, this study provides information for robust identification, scoring, and validation of TF targets using ChIP-based technologies.
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| 19. |
- Fontaine, N. K., et al.
(författare)
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Determination of 20 GHz InP AWG phase errors by measurement of AWG pulse train
- 2007
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Ingår i: 2007 IEEE LEOS Annual Meeting Conference Proceedings. - : IEEE. - 142440925X - 9781424409259 ; , s. 725-726
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Konferensbidrag (refereegranskat)abstract
- The phase errors of a 20 GHz AWG fabricated on InP are determined by measuring the intensity and phase of the pulse train produced by the transmission of a short pulse through an AWG.
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| 20. |
- Liu, Wing Kam, et al.
(författare)
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Complexity science of multiscale materials via stochastic computations
- 2009
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Ingår i: International Journal for Numerical Methods in Engineering. - : Wiley. - 0029-5981 .- 1097-0207. ; 80:6-7, s. 932-978
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Tidskriftsartikel (refereegranskat)abstract
- New technological advances today allow for a range of advanced composite materials, including multilayer materials and nanofiber-matrix composites. In this context, the key to developing advanced materials IS file understanding of the interplay between the various physical scales present. from the atomic level Interactions to the microstructaral composition and the marcoscale behavior Using the developing 'multiresolution data sets mechanics' the 'predictive science-based governing laws of the materials microstructure evolutions' are derived and Melted into a 'stochastic multiresolution design framework' Under such a framework. the governing laws Of the materials microstructure evolution will be essential to assess, across multiple scales. The impact of multiscale material design. geometry design of a structure and the manufacturing process conditions, by following the cause-effect relationship from structure property and then to performance The future Integrated multiscale analysis system will be Constructed based on a probabilistic complexity science-based mathematical framework. its verification, validation and uncertainty quantification tire done through carefully designed experiments, and file life-cycled materials design for products design and manufacturing is performed through the use of petascale computing. The various techniques of microstructure reconstruction result in the genetation of model microstructures that, at some level, has the same statistical properties as the real heterogenous media. Having reconstructed the heterogeneous medium. one can then evaluate Its effective properties via direct numerical simulation and compare these values with experimentally measured properties of the actual medium. The proposed analysis will be dynamic in nature to capture the multi-stage historical evolvement of material/structure performance over the life span of a product. In addition to providing more accurate assessment of structure performance with stochastic multiscale analysis. our development will provide the capability of predicting failures and system reliability to enable more reliable design and decisions in product development.
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| 21. |
- Lynch, S.A., et al.
(författare)
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Toward silicon-based lasers for terahertz sources
- 2006
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Ingår i: IEEE Journal of Selected Topics in Quantum Electronics. - 1077-260X .- 1558-4542. ; 12:6, s. 1570-1577
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Tidskriftsartikel (refereegranskat)abstract
- Producing an electrically pumped silicon-based laser at terahertz frequencies is gaining increased attention these days. This paper reviews the recent advances in the search for a silicon-based terahertz laser. Topics covered include resonant tunneling in p-type Si/SiGe, terahertz intersubband electroluminescence from quantum cascade structures, intersubband lifetime measurements in Si/SiGe quantum wells, enhanced optical guiding using buried suicide layers, and the potential for exploiting common impurity dopants in silicon such as boron and phosphorus to realize a terahertz laser. © 2006 IEEE.
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| 22. |
- Nath, Swapan K., et al.
(författare)
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A nonsynonymous functional variant in integrin-alpha(M) (encoded by ITGAM) is associated with systemic lupus erythematosus
- 2008
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 40:2, s. 152-154
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Tidskriftsartikel (refereegranskat)abstract
- We identified and replicated an association between ITGAM (CD11b) at 16p11.2 and risk of systemic lupus erythematosus (SLE) in 3,818 individuals of European descent. The strongest association was at a nonsynonymous SNP, rs1143679 (P = 1.7 x 10(-17), odds ratio = 1.78). We further replicated this association in two independent samples of individuals of African descent (P = 0.0002 and 0.003; overall meta-analysis P = 6.9 x 10(-22)). The genetic association between ITGAM and SLE implicates the alpha(M)beta2-integrin adhesion pathway in disease development.
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| 23. |
- Nuzhdin, K.B., et al.
(författare)
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Structure of radical cations of saturated heterocyclic compounds with two heteroatoms as studied by electron paramagnetic resonance, electron-nuclear double resonance, and density functional theory calculations
- 2005
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 109:28, s. 6166-6173
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Tidskriftsartikel (refereegranskat)abstract
- The radical cations of piperazine, morpholine, thiomorpholine, and thioxane were investigated by electron paramagnetic resonance (EPR) and electron-nuclear double resonance (ENDOR) spectroscopy in a solid Freon matrix. Optimized geometry and magnetic parameters of the radical cations were calculated using a density functional theory (DFT)/Perdew-Burke-Ernzerhof (PBE) method. Both experimental and theoretical results suggest that all the studied species adopt chair (or distorted chair) conformations. No evidence for the boat conformers with intramolecular σ*-bonding between heteroatoms were obtained. In the cases of morpholine and thioxane, the oxygen atoms are characterized by relatively small spin populations, whereas a major part of spin density is located at N and S atoms, respectively. The thiomorpholine radical cation exhibits nearly equal spin population of N and S atoms. In most cases (except for thioxane), the calculated magnetic parameters agree with the experimental data reasonably well. © 2005 American Chemical Society.
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| 24. |
- Prokopenko, Inga, et al.
(författare)
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Variants in MTNR1B influence fasting glucose levels
- 2009
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 41:1, s. 77-81
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Tidskriftsartikel (refereegranskat)abstract
- To identify previously unknown genetic loci associated with fasting glucose concentrations, we examined the leading association signals in ten genome-wide association scans involving a total of 36,610 individuals of European descent. Variants in the gene encoding melatonin receptor 1B (MTNR1B) were consistently associated with fasting glucose across all ten studies. The strongest signal was observed at rs10830963, where each G allele (frequency 0.30 in HapMap CEU) was associated with an increase of 0.07 (95% CI = 0.06-0.08) mmol/l in fasting glucose levels (P = 3.2 x 10(-50)) and reduced beta-cell function as measured by homeostasis model assessment (HOMA-B, P = 1.1 x 10(-15)). The same allele was associated with an increased risk of type 2 diabetes (odds ratio = 1.09 (1.05-1.12), per G allele P = 3.3 x 10(-7)) in a meta-analysis of 13 case-control studies totaling 18,236 cases and 64,453 controls. Our analyses also confirm previous associations of fasting glucose with variants at the G6PC2 (rs560887, P = 1.1 x 10(-57)) and GCK (rs4607517, P = 1.0 x 10(-25)) loci.
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| 25. |
- Rauter, P., et al.
(författare)
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Direct determination of ultrafast intersubband hole relaxation times in voltage biased SiGe quantum wells by a density matrix interpretation of femtosecond resolved photocurrent experiments
- 2007
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Ingår i: New Journal of Physics. - : Institute of Physics (IoP) and Deutsche Physikalische Gesellschaft. - 1367-2630. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- We report the quantitative and direct determination of hole intersubband relaxation times in a voltage biased SiGe heterostructure using density matrix calculations applied to a four-level system in order to interpret photocurrent (PC) pump-pump experiments. One consistent set of parameters allows the simulation of two kinds of experiments, namely pump-pump photocurrent experiments at a free electron laser (wavelength 7.9 mu m) and the laser-power dependence of the PC signal. This strongly confirms the high reliability of these parameter values, of which the most interesting in respect to Si based quantum cascade laser development is the extracted heavy-hole relaxation time. The simulations show that this relaxation time directly determines the experimentally observed decay of the pump-pump photocurrent signal as a function of the delay time. For a heavy hole intersubband spacing of 160 meV, a value of 550 fs was obtained. The experimental method was further applied to determine the LH1-HH1 relaxation time of a second sample with a transition energy below the optical phonon energy. The observed relaxation time of 16 ps is consistent with the value found for the same structure by transmission pump-probe experiments.
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| 26. |
- Saxena, Richa, et al.
(författare)
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Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels
- 2007
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 316:5829, s. 1331-1336
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Tidskriftsartikel (refereegranskat)abstract
- New strategies for prevention and treatment of type 2 diabetes (T2D) require improved insight into disease etiology. We analyzed 386,731 common single-nucleotide polymorphisms (SNPs) in 1464 patients with T2D and 1467 matched controls, each characterized for measures of glucose metabolism, lipids, obesity, and blood pressure. With collaborators (FUSION and WTCCC/UKT2D), we identified and confirmed three loci associated with T2D - in a noncoding region near CDKN2A and CDKN2B, in an intron of IGF2BP2, and an intron of CDKAL1 - and replicated associations near HHEX and in SLC30A8 found by a recent whole-genome association study. We identified and confirmed association of a SNP in an intron of glucokinase regulatory protein (GCKR) with serum triglycerides. The discovery of associated variants in unsuspected genes and outside coding regions illustrates the ability of genome-wide association studies to provide potentially important clues to the pathogenesis of common diseases.
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| 27. |
- Soares, F. M., et al.
(författare)
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Compact InP-Based 16-channel O-CDMA encoder/decoder
- 2007
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Ingår i: 2007 IEEE LEOS annual meeting conference proceedings. - : IEEE. - 142440925X - 9781424409259 ; , s. 723-724
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Konferensbidrag (refereegranskat)abstract
- A very compact InP-Based 16-channel O-CDMA encoder-/decoder chip (3.8mm × 6.8mm) has been designed, fabricated and characterized. The device successfully performs O-CDMA spectral encoding.
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| 28. |
- Springell, R., et al.
(författare)
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Elemental engineering : Epitaxial uranium thin films
- 2008
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 78:19
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Tidskriftsartikel (refereegranskat)abstract
- Epitaxial films of the well-known alpha (orthorhombic) structure and an unusual hcp form of uranium have been grown on Nb and Gd buffers, respectively, by sputtering techniques. In a 5000 A film of alpha-U a charge-density wave has been observed, and its properties are different from those found in the bulk. The 500 A hcp-U film has a c/a ratio of 1.90(1), which is unusually large for the hcp structure. Theoretical calculations show that this hcp form is metastable and predict that it orders magnetically.
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| 29. |
- Tamu Dufe, Veronica, et al.
(författare)
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Crystal structure of Plasmodium falciparum spermidine synthase in complex with the substrate decarboxylated S-adenosylmethionine and the potent inhibitors 4MCHA and AdoDATO
- 2007
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Ingår i: Journal of Molecular Biology. - : Elsevier BV. - 1089-8638 .- 0022-2836. ; 373:1, s. 167-177
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Tidskriftsartikel (refereegranskat)abstract
- Plasmodium falciparum is the causative agent of the most severe type of malaria, a life-threatening disease affecting the lives of over three billion people. Factors like widespread resistance against available drugs and absence of an effective vaccine are seriously compounding control of the malaria parasite. Thus, there is an urgent need for the identification and validation of new drug targets. The enzymes of the polyamine biosynthesis pathway have been suggested as possible targets for the treatment of malaria. One of these enzymes is spermidine synthase (SPDS, putrescine aminopropyltransferase), which catalyzes the transfer of an aminopropyl moiety from decarboxylated S-adenosylmethionine (dcAdoMet) to putrescine, leading to the formation of spermidine and 5 '-methylthioadenosine. Here we present the three-dimensional structure of P falciparum spermidine synthase (pfSPDS) in apo form, in complex with dcAdoMet and two inhibitors, S-adenosyl-1,8-diamino-3-thio-octane (AdoDATO) and trans-4-methylcyclohexylamine (4MCHA). The results show that binding of dcAdoMet to pfSPDS stabilizes the conformation of the flexible gatekeeper loop of the enzyme and affects the conformation of the active-site amino acid residues, preparing the protein for binding of the second substrate. The complexes of AdoDATO and 4MCHA with pfSPDS reveal the mode of interactions of these compounds with the enzyme. While AdoDATO essentially fills the entire active-site pocket, 4MCHA only occupies part of it, which suggests that simple modifications of this compound may yield more potent inhibitors of pfSPDS. (C) 2007 Elsevier Ltd. All rights reserved.
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| 30. |
- Tomlins, Scott A., et al.
(författare)
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The role of SPINK1 in ETS rearrangement-negative prostate cancers
- 2008
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Ingår i: Cancer Cell. - Amsterdam : Elsevier. - 1535-6108 .- 1878-3686. ; 13:6, s. 519-28
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Tidskriftsartikel (refereegranskat)abstract
- ETS gene fusions have been characterized in a majority of prostate cancers; however, the key molecular alterations in ETS-negative cancers are unclear. Here we used an outlier meta-analysis (meta-COPA) to identify SPINK1 outlier expression exclusively in a subset of ETS rearrangement-negative cancers ( approximately 10% of total cases). We validated the mutual exclusivity of SPINK1 expression and ETS fusion status, demonstrated that SPINK1 outlier expression can be detected noninvasively in urine, and observed that SPINK1 outlier expression is an independent predictor of biochemical recurrence after resection. We identified the aggressive 22RV1 cell line as a SPINK1 outlier expression model and demonstrate that SPINK1 knockdown in 22RV1 attenuates invasion, suggesting a functional role in ETS rearrangement-negative prostate cancers.
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| 31. |
- Wei, A., et al.
(författare)
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Differentiation of rodent bone marrow mesenchymal stem cells into intervertebral disc-like cells following coculture with rat disc tissue
- 2009
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Ingår i: Tissue Engineering Part A. - 1937-335X. ; 15:9, s. 2581-95
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Tidskriftsartikel (refereegranskat)abstract
- This study aimed to evaluate whether rat mesenchymal stem cells (rMSCs) could be differentiated in vitro into disc-like cells by coculturing with intervertebral disc tissue. rMSCs were cultured with rodent intervertebral disc for up to 30 days in transwell plates. The differentiation of rMSCs was evaluated by immunostaining, Western blot, real-time RT-PCR, Northern blot, and electron microscopy. The potentials of multilineage differentiation and proteoglycan and collagen synthesis were also investigated. rMSCs underwent morphological changes to form three-dimensional micromasses and expressed collagen-2, aggrecan, and sox-9 at RNA and protein levels after 14 days of coculture. These changes were not detected in the samples of rMSCs cultured alone. Cocultured rMSCs also showed other characteristic features of disc-like cells, including the extracellular matrix formation, and proteoglycan and collagen synthesis. In addition, cellular contact between cocultured rMSCs and disc tissue was observed by electron microscopy. Committed rMSCs still retained their differentiation ability into mesoderm lineages of adipocytes or osteocytes when the local environment was altered. This study supports that MSCs are a promising source for cell therapy and tissue engineering in disc regeneration, and highlights that rMSCs can be induced into nucleus pulposus-like cells in vitro under the direct influence of intact disc tissue.
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| 32. |
- Zhao, Ming, et al.
(författare)
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Strain-symmetrized Si/SiGe multi-quantum well structures grown by molecular beam epitaxy for intersubband engineering
- 2006
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Ingår i: Journal of luminescence. - : Elsevier BV. - 0022-2313. ; 121:2, s. 403-408
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Tidskriftsartikel (refereegranskat)abstract
- Three strain-symmetrized Si/SiGe multi-quantum well structures, designed for probing the carrier lifetime of intrawell intersubband transitions between heavy hole 1 (HH1) and light hole 1 (LH1) states with transition energies below the optical phonon energy, were grown by molecular beam epitaxy at low temperature on fully relaxed SiGe virtual substrates. The grown structures were characterized by using various experimental techniques, showing a high crystalline quality and very precise growth control. The lifetime of the LH1 excited state was determined directly with pump-probe spectroscopy. The measurements indicated an increase of the lifetime by a factor of 2 due to the increasingly unconfined LH1 state, which agreed very well with the design. It also showed a very long lifetime of several hundred picoseconds for the holes excited out of the well to transit back to the well through a diagonal process.
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