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| 7. |
- Aad, G, et al.
(författare)
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- 2015
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swepub:Mat__t
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| 8. |
- Park, J, et al.
(författare)
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Gene-Environment Interactions Relevant to Estrogen and Risk of Breast Cancer: Can Gene-Environment Interactions Be Detected Only among Candidate SNPs from Genome-Wide Association Studies?
- 2021
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Ingår i: Cancers. - : MDPI AG. - 2072-6694. ; 13:10
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Tidskriftsartikel (refereegranskat)abstract
- In this study we aim to examine gene–environment interactions (GxEs) between genes involved with estrogen metabolism and environmental factors related to estrogen exposure. GxE analyses were conducted with 1970 Korean breast cancer cases and 2052 controls in the case-control study, the Seoul Breast Cancer Study (SEBCS). A total of 11,555 SNPs from the 137 candidate genes were included in the GxE analyses with eight established environmental factors. A replication test was conducted by using an independent population from the Breast Cancer Association Consortium (BCAC), with 62,485 Europeans and 9047 Asians. The GxE tests were performed by using two-step methods in GxEScan software. Two interactions were found in the SEBCS. The first interaction was shown between rs13035764 of NCOA1 and age at menarche in the GE|2df model (p-2df = 1.2 × 10−3). The age at menarche before 14 years old was associated with the high risk of breast cancer, and the risk was higher when subjects had homozygous minor allele G. The second GxE was shown between rs851998 near ESR1 and height in the GE|2df model (p-2df = 1.1 × 10−4). Height taller than 160 cm was associated with a high risk of breast cancer, and the risk increased when the minor allele was added. The findings were not replicated in the BCAC. These results would suggest specificity in Koreans for breast cancer risk.
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| 10. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 11. |
- Kang, JS, et al.
(författare)
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Risk prediction for malignant intraductal papillary mucinous neoplasm of the pancreas: logistic regression versus machine learning
- 2020
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1, s. 20140-
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Tidskriftsartikel (refereegranskat)abstract
- Most models for predicting malignant pancreatic intraductal papillary mucinous neoplasms were developed based on logistic regression (LR) analysis. Our study aimed to develop risk prediction models using machine learning (ML) and LR techniques and compare their performances. This was a multinational, multi-institutional, retrospective study. Clinical variables including age, sex, main duct diameter, cyst size, mural nodule, and tumour location were factors considered for model development (MD). After the division into a MD set and a test set (2:1), the best ML and LR models were developed by training with the MD set using a tenfold cross validation. The test area under the receiver operating curves (AUCs) of the two models were calculated using an independent test set. A total of 3,708 patients were included. The stacked ensemble algorithm in the ML model and variable combinations containing all variables in the LR model were the most chosen during 200 repetitions. After 200 repetitions, the mean AUCs of the ML and LR models were comparable (0.725 vs. 0.725). The performances of the ML and LR models were comparable. The LR model was more practical than ML counterpart, because of its convenience in clinical use and simple interpretability.
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| 13. |
- Bravo, L, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 15. |
- Adcox, K, et al.
(författare)
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Formation of dense partonic matter in relativistic nucleus-nucleus collisions at RHIC: Experimental evaluation by the PHENIX Collaboration
- 2005
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Ingår i: Nuclear Physics, Section A. - : Elsevier BV. - 0375-9474. ; 757:1-2, s. 184-283
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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.
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| 16. |
- Adler, SS, et al.
(författare)
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Bose-Einstein correlations of charged pion pairs in Au+Au collisions at root(NN)-N-s = 200 GeV
- 2004
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Ingår i: Physical Review Letters. - 1079-7114. ; 93:15
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Tidskriftsartikel (refereegranskat)abstract
- Bose-Einstein correlations of identically charged pion pairs were measured by the PHENIX experiment at midrapidity in Au+Au collisions at roots(NN)=200 GeV. The Bertsch-Pratt radius parameters were determined as a function of the transverse momentum of the pair and as a function of the centrality of the collision. Using the standard core-halo partial Coulomb fits, and a new parametrization which constrains the Coulomb fraction as determined from the unlike-sign pion correlation, the ratio R-out/R-side is within 0.8-1.1 for 0.25<<1.2 GeV/c. The centrality dependence of all radii is well described by a linear scaling in N-part(1/3), and R-out/R-side for similar to0.45 GeV/c is approximately constant at unity as a function of centrality.
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| 18. |
- Adler, SS, et al.
(författare)
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Common suppression pattern of eta and pi(0) mesons at high transverse momentum in Au plus Au collisions at root SNN=200 GeV
- 2006
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Ingår i: Physical Review Letters. - 1079-7114. ; 96:20
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Tidskriftsartikel (refereegranskat)abstract
- Inclusive transverse momentum spectra of eta mesons have been measured within p(T)=2-10 GeV/c at midrapidity by the PHENIX experiment in Au+Au collisions at root s(NN) = 200 GeV. In central Au+Au the eta yields are significantly suppressed compared to peripheral Au+Au, d+Au, and p+p yields scaled by the corresponding number of nucleon-nucleon collisions. The magnitude, centrality, and p(T) dependence of the suppression is common, within errors, for eta and pi(0). The ratio of eta to pi(0) spectra at high p(T) amounts to 0.40 < R-eta/pi(0)< 0.48 for the three systems, in agreement with the world average measured in hadronic and nuclear reactions and, at large scaled momentum, in e(+)e(-) collisions.
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| 19. |
- Adler, SS, et al.
(författare)
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Deuteron and antideuteron production in Au+Au collisions at root s(NN)=200 GeV
- 2005
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Ingår i: Physical Review Letters. - 1079-7114. ; 94:12
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Tidskriftsartikel (refereegranskat)abstract
- The production of deuterons and antideuterons in the transverse momentum range 1.1 < p(T)< 4.3 GeV/c at midrapidity in Au+Au collisions at root s(NN) = 200 GeV has been studied by the PHENIX experiment at RHIC. A coalescence analysis, comparing the deuteron and antideuteron spectra with that of proton and antiproton, has been performed. The coalescence probability is equal for both deuterons and antideuterons and it increases as a function of p(T), which is consistent with an expanding collision zone. Comparing (anti)proton yields, (p) over bar /p = 0.73 +/- 0.01, with (anti)deuteron yields, (d) over bar /d = 0.47 +/- 0.03, we estimate that (n) over bar /n = 0.64 +/- 0.04. The nucleon phase space density is estimated from the coalescence measurement.
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| 20. |
- Adler, SS, et al.
(författare)
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Elliptic flow of identified hadrons in Au+Au collisions at root s(NN)=200 GeV
- 2003
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Ingår i: Physical Review Letters. - 1079-7114. ; 91:18: 182301
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Tidskriftsartikel (refereegranskat)abstract
- The anisotropy parameter (v(2)), the second harmonic of the azimuthal particle distribution, has been measured with the PHENIX detector in Au+Au collisions at roots(NN)=200 GeV for identified and inclusive charged particle production at central rapidities (eta<0.35) with respect to the reaction plane defined at high rapidities (eta=3-4 ). We observe that the v(2) of mesons falls below that of (anti)baryons for p(T)>2 GeV/c, in marked contrast to the predictions of a hydrodynamical model. A quark-coalescence model is also investigated.
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| 21. |
- Adler, SS, et al.
(författare)
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J/psi production from proton-proton collisions at root s=200 GeV
- 2004
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Ingår i: Physical Review Letters. - 1079-7114. ; 92:5
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Tidskriftsartikel (refereegranskat)abstract
- J/psi production has been measured in proton-proton collisions at roots=200 GeV over a wide rapidity and transverse momentum range by the PHENIX experiment at the Relativistic Heavy Ion Collider. Distributions of the rapidity and transverse momentum, along with measurements of the mean transverse momentum and total production cross section are presented and compared to available theoretical calculations. The total J/psi cross section is 4.0+/-0.6(stat)+/-0.6(syst)+/-0.4(abs) mub. The mean transverse momentum is 1.80+/-0.23(stat)+/-0.16(syst) GeV/c.
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| 22. |
- Adler, SS, et al.
(författare)
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J/psi production in Au-Au collisions at root s(NN)=200 GeV
- 2004
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Ingår i: Physical Review C (Nuclear Physics). - 0556-2813. ; 69:1
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Tidskriftsartikel (refereegranskat)abstract
- First results on charm quarkonia production in heavy ion collisions at the Relativistic Heavy Ion Collider (RHIC) are presented. The yield of J/psi's measured in the PHENIX experiment via electron-positron decay pairs at midrapidity for Au-Au reactions at roots(NN) = 200 GeV is analyzed as a function of collision centrality. For this analysis we have studied 49.3x10(6) minimum bias Au-Au reactions. We present the J/psi invariant yield dN/dy for peripheral and midcentral reactions. For the most central collisions where we observe no signal above background, we quote 90% confidence level upper limits. We compare these results with our J/psi measurement from proton-proton reactions at the same energy. We find that our measurements are not consistent with models that predict strong enhancement relative to binary collision scaling.
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| 23. |
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| 24. |
- Adler, SS, et al.
(författare)
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Measurement of single electron event anisotropy in Au plus Au collisions at root s(NN)=200 GeV
- 2005
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Ingår i: Physical Review C (Nuclear Physics). - 0556-2813. ; 72:2
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Tidskriftsartikel (refereegranskat)abstract
- The transverse momentum dependence of the azimuthal anisotropy parameter v(2), the second harmonic of the azimuthal distribution, for electrons at midrapidity (vertical bar eta vertical bar < 0.35) has been measured with the PHENIX detector in Au+Au collisions at root s(NN) = 200 GeV. The measurement was made with respect to the reaction plane defined at high rapidities (vertical bar eta vertical bar = 3.1-3.9). From the result we have measured the v(2) of electrons from heavy flavor decay after subtraction of the v(2) of electrons from other sources such as photon conversions and Dalitz decay from light neutral mesons. We observe a nonzero single electron v(2) with a 90% confidence level in the intermediate-p(T) region. The precision of the present data set does not permit us to conclude definitively that heavy quarks exhibit thermalization with the transverse flow of the bulk matter.
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| 25. |
- Adler, SS, et al.
(författare)
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Measurement of transverse single-spin asymmetries for midrapidity production of neutral pions and charged hadrons in polarized p+p collisions at root s=200 GeV
- 2005
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Ingår i: Physical Review Letters. - 1079-7114. ; 95
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Tidskriftsartikel (refereegranskat)abstract
- Transverse single-spin asymmetries to probe the transverse-spin structure of the proton have been measured for neutral pions and nonidentified charged hadrons from polarized proton-proton collisions at midrapidity and root s = 200 GeV. The data cover a transverse momentum (pT) range 1.0-5.0 GeV/c for neutral pions and 0.5-5.0 GeV/c for charged hadrons, at a Feynman-x value of approximately zero. The asymmetries seen in this previously unexplored kinematic region are consistent with zero within errors of a few percent. In addition, the inclusive charged hadron cross section at midrapidity from 0.5 < P-T < 7.0 GeV/c is presented and compared to next-to-leading order perturbative QCD ( pQCD) calculations. Successful description of the unpolarized cross section above similar to 2 GeV/c suggests that pQCD is applicable in the interpretation of the asymmetry results in the relevant kinematic range.
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