1. |
- Adare, A., et al.
(author)
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Medium Modification of Jet Fragmentation in Au plus Au Collisions at root S-NN=200 GeV Measured in Direct Photon-Hadron Correlations
- 2013
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In: Physical Review Letters. - 1079-7114. ; 111:3
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Journal article (peer-reviewed)abstract
- The jet fragmentation function is measured with direct photon-hadron correlations in p + p and Au + Au collisions at root S-NN = 200 GeV. The P-T of the photon is an excellent approximation to the initial P-T of the jet and the ratio Z(T) = P-T(h)/P-T(gamma) is used as a proxy for the jet fragmentation function. A statistical subtraction is used to extract the direct photon-hadron yields in Au + Au collisions while a photon isolation cut is applied in p + p. I-AA, the ratio of hadron yield opposite the photon in Au + Au to that in p + p, indicates modification of the jet fragmentation function. Suppression, most likely due to energy loss in the medium, is seen at high Z(T). The associated hadron yield at low Z(T) is enhanced at large angles. Such a trend is expected from redistribution of the lost energy into increased production of low-momentum particles.
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2. |
- Adare, A., et al.
(author)
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Measurement of higher cumulants of net-charge multiplicity distributions in Au plus Au collisions at root s(NN)=7.7-200 GeV
- 2016
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In: Physical Review C (Nuclear Physics). - 0556-2813. ; 93:1
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Journal article (peer-reviewed)abstract
- We report the measurement of cumulants (C-n,n = 1, ..., 4) of the net-charge distributions measured within pseudorapidity (vertical bar eta vertical bar < 0.35) in Au + Au collisions at root s(NN) = 7.7-200 GeV with the PHENIX experiment at the Relativistic Heavy Ion Collider. The ratios of cumulants (e.g., C-1/C-2, C-3/C-1) of the net-charge distributions, which can be related to volume independent susceptibility ratios, are studied as a function of centrality and energy. These quantities are important to understand the quantum-chromodynamics phase diagram and possible existence of a critical end point. The measured values are very well described by expectation from negative binomial distributions. We do not observe any nonmonotonic behavior in the ratios of the cumulants as a function of collision energy. The measured values of C-1/C-2 and C-3/C-1 can be directly compared to lattice quantum-chromodynamics calculations and thus allow extraction of both the chemical freeze-out temperature and the baryon chemical potential at each center-of-mass energy. The extracted baryon chemical potentials are in excellent agreement with a thermal-statistical analysis model.
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3. |
- Adare, A., et al.
(author)
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Measurement of gamma(1S+2S+3S) production in p plus p and Au plus Au collisions at root sNN=200 GeV
- 2015
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In: Physical Review C (Nuclear Physics). - 0556-2813. ; 91:2
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Journal article (peer-reviewed)abstract
- Measurements of bottomonium production in heavy-ion and p + p collisions at the Relativistic Heavy Ion Collider (RHIC) are presented. The inclusive yield of the three states, (1S + 2S + 3S), was measured in the PHENIX experiment via electron-positron decay pairs at midrapidity for Au + Au and p + p collisions at root sNN = 200 GeV. The (1S + 2S + 3S) -> e(+)e(-) differential cross section at midrapidity was found to be B(ee)d sigma/dy = 108 +/- 38 (stat) +/- 15 (syst) +/- 11 (luminosity) pb in p + p collisions. The nuclear modification factor in the 30% most central Au + Au collisions indicates a suppression of the total. state yield relative to the extrapolation from p + p collision data. The suppression is consistent with measurements made by STAR at RHIC and at higher energies by the CMS experiment at the Large Hadron Collider.
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4. |
- Adare, A., et al.
(author)
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Centrality dependence of low-momentum direct-photon production in Au plus Au collisions at root s(NN)=200 GeV
- 2015
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In: Physical Review C (Nuclear Physics). - 0556-2813. ; 91:6
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Journal article (peer-reviewed)abstract
- The PHENIX experiment at RHIC has measured the centrality dependence of the direct photon yield from Au + Au collisions at root s(NN) = 200 GeV down to pT = 0.4 GeV/c. Photons are detected via photon conversions to e(+)e(-) pairs and an improved technique is applied that minimizes the systematic uncertainties that usually limit direct photon measurements, in particular at low pT. We find an excess of direct photons above the N-coll-scaled yield measured in p + p collisions. This excess yield is well described by an exponential distribution with an inverse slope of about 240 MeV/c in the pT range 0.6-2.0 GeV/c. While the shape of the pT distribution is independent of centrality within the experimental uncertainties, the yield increases rapidly with increasing centrality, scaling approximately with N-part(alpha), where alpha = 1.38 +/- 0.03(stat) +/- 0.07(syst).
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5. |
- Adare, A., et al.
(author)
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Evolution of pi(0) Suppression in Au plus Au Collisions from root s(NN)=39 to 200 GeV
- 2012
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In: Physical Review Letters. - 1079-7114. ; 109:15
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Journal article (peer-reviewed)abstract
- Neutral-pion pi(0) spectra were measured at midrapidity (vertical bar y vertical bar < 0.35) in Au + Au collisions at root s(NN) = 39 and 62.4 GeV and compared with earlier measurements at 200 GeV in a transverse-momentum range of 1 < p(T) < 10 GeV/c. The high-p(T) tail is well described by a power law in all cases, and the powers decrease significantly with decreasing center-of-mass energy. The change of powers is very similar to that observed in the corresponding spectra for p + p collisions. The nuclear modification factors (RAA) show significant suppression, with a distinct energy, centrality, and p(T) dependence. Above p(T) = 7 GeV/c, R-AA is similar for root sNN = 62.4 and 200 GeV at all centralities. Perturbative-quantum-chromodynamics calculations that describe R-AA well at 200 GeV fail to describe the 39 GeV data, raising the possibility that, for the same p(T) region, the relative importance of initial-state effects and soft processes increases at lower energies. The p(T) range where pi(0) spectra in central Au + Au collisions have the same power as in p + p collisions is approximate to 5 and 7 GeV/c for root sNN = 200 and 62.4 GeV, respectively. For the root sNN = 39 GeV data, it is not clear whether such a region is reached, and the x(T) dependence of the x(T)-scaling power-law exponent is very different from that observed in the root sNN = 62 and 200 GeV data, providing further evidence that initial-state effects and soft processes mask the in-medium suppression of hardscattered partons to higher p(T) as the collision energy decreases.
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6. |
- Adare, A., et al.
(author)
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Heavy-quark production and elliptic flow in Au plus Au collisions at root(NN)-N-S=62.4 GeV
- 2015
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In: Physical Review C (Nuclear Physics). - 0556-2813. ; 91:4
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Journal article (peer-reviewed)abstract
- We present measurements of electrons and positrons from the semileptonic decays of heavy-flavor hadrons at midrapidity (vertical bar gamma vertical bar < 0.35) in Au + Au collisions at root(NN)-N-S = 62.4 GeV. The data were collected in 2010 by the PHENIX experiment that included the new hadron-blind detector. The invariant yield of electrons from heavy-flavor decays is measured as a function of transverse momentum in the range 1 < p(T)(e) < 5 GeV/c. The invariant yield per binary collision is slightly enhanced above the p + p reference in Au + Au 0%-20%, 20%-40%, and 40%-60% centralities at a comparable level. At this low beam energy this may be a result of the interplay between initial-state Cronin effects, final-state flow, and energy loss in medium. The v(2) of electrons from heavy-flavor decays is nonzero when averaged between 1.3 < p(T)(e) < 2.5 GeV/c for 0%-40% centrality collisions at root(NN)-N-S = 62.4 GeV. For 20%-40% centrality collisions, the v(2) at root(NN)-N-S = 62.4 GeV is smaller than that for heavy-flavor decays at root(NN)-N-S = 200 GeV. The v2 of the electrons from heavy-flavor decay at the lower beam energy is also smaller than v(2) for pions. Both results indicate that the heavy quarks interact with the medium formed in these collisions, but they may not be at the same level of thermalization with the medium as observed at root(NN)-N-S = 200 GeV.
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7. |
- Adare, A., et al.
(author)
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J/psi suppression at forward rapidity in Au plus Au collisions at root s(NN)=39 and 62.4 GeV
- 2012
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In: Physical Review C (Nuclear Physics). - 0556-2813. ; 86:6
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Journal article (peer-reviewed)abstract
- We present measurements of the J/psi invariant yields in root s(NN) = 39 and 62.4 GeV Au + Au collisions at forward rapidity (1.2 < vertical bar y vertical bar < 2.2). Invariant yields are presented as a function of both collision centrality and transverse momentum. Nuclear modifications are obtained for central relative to peripheral Au + Au collisions (R-CP) and for various centrality selections in Au + Au relative to scaled p + p cross sections obtained from other measurements (R-AA). The observed suppression patterns at 39 and 62.4 GeV are quite similar to those previously measured at 200 GeV. This similar suppression presents a challenge to theoretical models that contain various competing mechanisms with different energy dependencies, some of which cause suppression and others enhancement. DOI: 10.1103/PhysRevC.86.064901
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8. |
- Hudeček, Jan, et al.
(author)
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Application of a risk-management framework for integration of stromal tumor-infiltrating lymphocytes in clinical trials
- 2020
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In: npj Breast Cancer. - : Springer Science and Business Media LLC. - 2374-4677. ; 6:1
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Research review (peer-reviewed)abstract
- Stromal tumor-infiltrating lymphocytes (sTILs) are a potential predictive biomarker for immunotherapy response in metastatic triple-negative breast cancer (TNBC). To incorporate sTILs into clinical trials and diagnostics, reliable assessment is essential. In this review, we propose a new concept, namely the implementation of a risk-management framework that enables the use of sTILs as a stratification factor in clinical trials. We present the design of a biomarker risk-mitigation workflow that can be applied to any biomarker incorporation in clinical trials. We demonstrate the implementation of this concept using sTILs as an integral biomarker in a single-center phase II immunotherapy trial for metastatic TNBC (TONIC trial, NCT02499367), using this workflow to mitigate risks of suboptimal inclusion of sTILs in this specific trial. In this review, we demonstrate that a web-based scoring platform can mitigate potential risk factors when including sTILs in clinical trials, and we argue that this framework can be applied for any future biomarker-driven clinical trial setting.
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9. |
- Nederlof, M. A. J., et al.
(author)
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Application of polychaetes in (de)coupled integrated aquaculture: production of a high-quality marine resource
- 2019
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In: Aquaculture Environment Interactions. - : Inter-Research Science Center. - 1869-215X .- 1869-7534. ; 11, s. 221-237
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Journal article (peer-reviewed)abstract
- Capitella sp. and Ophryotrocha craigsmithi received a diet of salmon feces to evaluate their potential to convert fish waste into valuable marine products, e.g. ingredients for fish feed formulation. Production rate and body composition (focusing on fatty acid [FA] profiles) were determined for polychaetes fed fresh, acid-preserved or oven-dried salmon feces to evaluate their application in (de)coupled integrated multi-trophic aquaculture (IMTA) systems. Coupled production refers to direct integration of fish and polychaetes within the same (eco)system, while in decoupled production, units can be spatially or functionally separated. For decoupled production, preservation of fish waste is recommended. Although diets contained relatively low polyunsaturated FA (PUFA) levels (5-9% of total FAs), both species were rich in PUFAs (>30% of total FAs) and contained the essential FAs for fish. Feeding Capitella sp. the acid-preserved diet enriched its FA profile. Accumulation of PUFAs, de novo synthesis and/or transfer via bacterial biomass could have played a role in the upregulation of PUFA content. Amino acid profiles indicated that these polychaetes contained the amino acids essential for fish. Highest growth for both species was observed when fed fresh feces, whereas preserved diets resulted in negative growth rates for O. craigsmithi, suggesting an important role of microbes in polychaete diets. Our results indicate that both species are potential valuable marine products. Given growth rates with different diets, O. craigsmithi seems more suitable for integration in coupled systems, while Capitella sp. is interesting for both coupled and decoupled integrated systems.
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10. |
- Jansen, H. M., et al.
(author)
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Enhancing opportunistic polychaete communities under fish farms: an alternative concept for integrated aquaculture
- 2019
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In: Aquaculture Environment Interactions. - : Inter-Research Science Center. - 1869-215X .- 1869-7534. ; 11, s. 331-336
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Journal article (peer-reviewed)abstract
- This note presents the development of benthic integrated aquaculture, addressing a novel cultivation concept for open-water aquaculture. We introduce an approach that supports the colonization of indigenous polychaete communities on benthic cultivation trays deployed in the vicinity of fish-farming cages. Enhancement and subsequent harvest of polychaetes that naturally dominate the local benthic response is essentially different from the classical IMTA approach wherein juveniles and/or seedlings of the extractive species are introduced to the farm site. Results of a field trial showed quick and massive colonization of cultivation trays by polychaetes (predominantly Ophryotrocha craigsmithi) and large spatial variability within the salmon farm site. Our results suggest that enhancing indigenous opportunistic polychaetes is a promising cultivation concept making use of the deposition of organic wastes such as fish faeces and uneaten feed. The methods and results presented here contribute to solutions for technical optimization of benthic IMTA techniques. We expect that further advances in benthic IMTA production will contribute to the expansion of open-water finfish aquaculture within environmentally sustainable boundaries.
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11. |
- Van Bockstal, MR, et al.
(author)
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Interobserver Agreement of PD-L1/SP142 Immunohistochemistry and Tumor-Infiltrating Lymphocytes (TILs) in Distant Metastases of Triple-Negative Breast Cancer: A Proof-of-Concept Study. A Report on Behalf of the International Immuno-Oncology Biomarker Working Group
- 2021
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In: Cancers. - : MDPI AG. - 2072-6694. ; 13:19
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Journal article (peer-reviewed)abstract
- Patients with advanced triple-negative breast cancer (TNBC) benefit from treatment with atezolizumab, provided that the tumor contains ≥1% of PD-L1/SP142-positive immune cells. Numbers of tumor-infiltrating lymphocytes (TILs) vary strongly according to the anatomic localization of TNBC metastases. We investigated inter-pathologist agreement in the assessment of PD-L1/SP142 immunohistochemistry and TILs. Ten pathologists evaluated PD-L1/SP142 expression in a proficiency test comprising 28 primary TNBCs, as well as PD-L1/SP142 expression and levels of TILs in 49 distant TNBC metastases with various localizations. Interobserver agreement for PD-L1 status (positive vs. negative) was high in the proficiency test: the corresponding scores as percentages showed good agreement with the consensus diagnosis. In TNBC metastases, there was substantial variability in PD-L1 status at the individual patient level. For one in five patients, the chance of treatment was essentially random, with half of the pathologists designating them as positive and half negative. Assessment of PD-L1/SP142 and TILs as percentages in TNBC metastases showed poor and moderate agreement, respectively. Additional training for metastatic TNBC is required to enhance interobserver agreement. Such training, focusing on metastatic specimens, seems worthwhile, since the same pathologists obtained high percentages of concordance (ranging from 93% to 100%) on the PD-L1 status of primary TNBCs.
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