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1.	Adare, A., et al. (författare) Measurements of Elliptic and Triangular Flow in High-Multiplicity He-3 + Au Collisions at root s(NN)=200 GeV 2015 Ingår i: Physical Review Letters. - 1079-7114. ; 115:14 Tidskriftsartikel (refereegranskat)abstract We present the first measurement of elliptic (v(2)) and triangular (v(3)) flow in high-multiplicity He-3 + Au collisions at root s(NN) = 200 GeV. Two-particle correlations, where the particles have a large separation in pseudorapidity, are compared in He-3 + Au and in p + p collisions and indicate that collective effects dominate the second and third Fourier components for the correlations observed in the He-3 + Au system. The collective behavior is quantified in terms of elliptic v(2) and triangular v(3) anisotropy coefficients measured with respect to their corresponding event planes. The v(2) values are comparable to those previously measured in d + Au collisions at the same nucleon-nucleon center-of-mass energy. Comparisons with various theoretical predictions are made, including to models where the hot spots created by the impact of the three He-3 nucleons on the Au nucleus expand hydrodynamically to generate the triangular flow. The agreement of these models with data may indicate the formation of low-viscosity quark-gluon plasma even in these small collision systems.
2.	Adare, A., et al. (författare) Search for dark photons from neutral meson decays in p plus p and d plus Au collisions at root s(NN)=200 GeV 2015 Ingår i: Physical Review C (Nuclear Physics). - 0556-2813. ; 91:3 Tidskriftsartikel (refereegranskat)abstract The standard model (SM) of particle physics is spectacularly successful, yet the measured value of the muon anomalous magnetic moment (g - 2)mu deviates from SM calculations by 3.6 sigma. Several theoretical models attribute this to the existence of a "dark photon," an additional U(1) gauge boson, which is weakly coupled to ordinary photons. The PHENIX experiment at the Relativistic Heavy Ion Collider has searched for a dark photon, U, in pi(0), eta -> gamma e(+)e(-) decays and obtained upper limits of O(2 x 10(-6)) on U-gamma mixing at 90% C.L. for the mass range 30 < m(U) < 90 MeV/c(2). Combined with other experimental limits, the remaining region in the U-gamma mixing parameter space that can explain the (g - 2)(mu) deviation from its SM value is nearly completely excluded at the 90% confidence level, with only a small region of 29 < m(U) < 32 MeV/c(2) remaining.
3.	Adare, A., et al. (författare) Medium Modification of Jet Fragmentation in Au plus Au Collisions at root S-NN=200 GeV Measured in Direct Photon-Hadron Correlations 2013 Ingår i: Physical Review Letters. - 1079-7114. ; 111:3 Tidskriftsartikel (refereegranskat)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.
4.	Adare, A., et al. (författare) Measurement of higher cumulants of net-charge multiplicity distributions in Au plus Au collisions at root s(NN)=7.7-200 GeV 2016 Ingår i: Physical Review C (Nuclear Physics). - 0556-2813. ; 93:1 Tidskriftsartikel (refereegranskat)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.
5.	Adare, A., et al. (författare) gamma (1S+2S+3S) production in d plus Au and p plus p collisions at root s(NN)=200 GeV and cold-nuclear-matter effects 2013 Ingår i: Physical Review C (Nuclear Physics). - 0556-2813. ; 87:4 Tidskriftsartikel (refereegranskat)abstract The three gamma states, gamma (1S + 2S + 3S), are measured in d + Au and p + p collisions at root s(NN) = 200 GeV and rapidities 1.2 < vertical bar y vertical bar < 2.2 by the PHENIX experiment at the Relativistic Heavy Ion Collider. Cross sections for the inclusive gamma (1S + 2S + 3S) production are obtained. The inclusive yields per binary collision for d + Au collisions relative to those in p + p collisions (R-dAu) are found to be 0.62 +/- 0.26 (stat) +/- 0.13 (syst) in the gold-going direction and 0.91 +/- 0.33 (stat) +/- 0.16 (syst) in the deuteron-going direction. The measured results are compared to a nuclear-shadowing model, EPS09 [Eskola et al., J. High Energy Phys. 04 (2009) 065], combined with a final-state breakup cross section, sigma(br), and compared to lower energy p + A results. We also compare the results to the PHENIX J/psi results [Adare et al., Phys. Rev. Lett. 107, 142301 (2011)]. The rapidity dependence of the observed gamma suppression is consistent with lower energy p + A measurements. DOI: 10.1103/PhysRevC.87.044909
6.	Adare, A., et al. (författare) Measurement of gamma(1S+2S+3S) production in p plus p and Au plus Au collisions at root sNN=200 GeV 2015 Ingår i: Physical Review C (Nuclear Physics). - 0556-2813. ; 91:2 Tidskriftsartikel (refereegranskat)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.
7.	Adare, A., et al. (författare) Centrality dependence of low-momentum direct-photon production in Au plus Au collisions at root s(NN)=200 GeV 2015 Ingår i: Physical Review C (Nuclear Physics). - 0556-2813. ; 91:6 Tidskriftsartikel (refereegranskat)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).
8.	Adare, A., et al. (författare) Cold Nuclear Matter Effects on J/psi Yields as a Function of Rapidity and Nuclear Geometry in d plus A Collisions at root S-NN=200 GeV 2011 Ingår i: Physical Review Letters. - 1079-7114. ; 107:14 Tidskriftsartikel (refereegranskat)abstract We present measurements of J/psi yields in d + Au collisions at root S-NN = 200 GeV recorded by the PHENIX experiment and compare them with yields in p + p collisions at the same energy per nucleon-nucleon collision. The measurements cover a large kinematic range in J/psi rapidity (-2.2 < y < 2.4) with high statistical precision and are compared with two theoretical models: one with nuclear shadowing combined with final state breakup and one with coherent gluon saturation effects. In order to remove model dependent systematic uncertainties we also compare the data to a simple geometric model. The forward rapidity data are inconsistent with nuclear modifications that are linear or exponential in the density weighted longitudinal thickness, such as those from the final state breakup of the bound state.
9.	Adare, A., et al. (författare) Measurement of transverse-single-spin asymmetries for midrapidity and forward-rapidity production of hadrons in polarized p plus p collisions at root s=200 and 62.4 GeV 2014 Ingår i: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368. ; 90:1 Tidskriftsartikel (refereegranskat)abstract Measurements of transverse-single-spin asymmetries (A(N)) in p + p collisions at root s = 62.4 and 200 GeV with the PHENIX detector at the Relativistic Heavy Ion Collider are presented. At midrapidity, A(N) is measured for neutral pion and eta mesons reconstructed from diphoton decay, and, at forward rapidities, neutral pions are measured using both diphotons and electromagnetic clusters. The neutral-pion measurement of A(N) at midrapidity is consistent with zero with uncertainties a factor of 20 smaller than previous publications, which will lead to improved constraints on the gluon Sivers function. At higher rapidities, where the valence quark distributions are probed, the data exhibit sizable asymmetries. In comparison with previous measurements in this kinematic region, the new data extend the kinematic coverage in root s and p(T), and it is found that the asymmetries depend only weakly on root s. The origin of the forward A(N) is presently not understood quantitatively. The extended reach to higher p(T) probes the transition between transverse momentum dependent effects at low p(T) and multiparton dynamics at high p(T).
10.	Adare, A., et al. (författare) Low-mass vector-meson production at forward rapidity in p plus p collisions at root s=200 GeV 2014 Ingår i: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368. ; 90:5 Tidskriftsartikel (refereegranskat)abstract The PHENIX experiment at the Relativistic Heavy Ion Collider has measured low-mass vector-meson ,omega, rho, and phi, production through the dimuon decay channel at forward rapidity (1.2 < vertical bar y vertical bar < 2.2) in p + p collisions at root s = 200 GeV. The differential cross sections for these mesons are measured as a function of both p(T) and rapidity. We also report the integrated differential cross sections over 1 < p(T) < 7 GeV/c and 1.2 < vertical bar y vertical bar < 2.2: d sigma/dy(omega + rho rho -> mu mu) = 80 +/- 6(stat) +/- 12(syst)nb and d sigma/dy(phi -> mu mu) = 27 +/- 3(stat) +/- 4(syst)nb. These results are compared with midrapidity measurements and calculations.
11.	Adare, A., et al. (författare) Evolution of pi(0) Suppression in Au plus Au Collisions from root s(NN)=39 to 200 GeV 2012 Ingår i: Physical Review Letters. - 1079-7114. ; 109:15 Tidskriftsartikel (refereegranskat)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.
12.	Adare, A., et al. (författare) Cold-Nuclear-Matter Effects on Heavy-Quark Production at Forward and Backward Rapidity in d + Au Collisions at root s(NN) = GeV 2014 Ingår i: Physical Review Letters. - 1079-7114. ; 112:25 Tidskriftsartikel (refereegranskat)abstract The PHENIX experiment has measured open heavy-flavor production via semileptonic decay over the transverse momentum range 1 < p(T) < 6 GeV/c at forward and backward rapidity (1.4 < vertical bar y vertical bar < 2.0) in d + Au and p + p collisions at root s(NN) = 200 GeV. In central d + Au collisions, relative to the yield in p + p collisions scaled by the number of binary nucleon-nucleon collisions, a suppression is observed at forward rapidity (in the d-going direction) and an enhancement at backward rapidity (in the Au-going direction). Predictions using nuclear-modified-parton-distribution functions, even with additional nuclear-p(T) broadening, cannot simultaneously reproduce the data at both rapidity ranges, which implies that these models are incomplete and suggests the possible importance of final-state interactions in the asymmetric d + Au collision system. These results can be used to probe cold-nuclear-matter effects, which may significantly affect heavy-quark production, in addition to helping constrain the magnitude of charmonia-breakup effects in nuclear matter.
13.	Adare, A., et al. (författare) Cross Section and Parity-Violating Spin Asymmetries of W-+/- Boson Production in Polarized p plus p Collisions at root s=500 Gev 2011 Ingår i: Physical Review Letters. - 1079-7114. ; 106:6 Tidskriftsartikel (refereegranskat)abstract Large parity-violating longitudinal single-spin asymmetries A(L)(e+) = 0.86(-0.14)(+0.30) and Ae(L)(e-) = 0.88(-0.71)(+0.12) are observed for inclusive high transverse momentum electrons and positrons in polarized p + p collisions at a center-of-mass energy of root s = 500 GeV with the PHENIX detector at RHIC. These e(+/-) come mainly from the decay of W-+/- and Z(0) bosons, and their asymmetries directly demonstrate parity violation in the couplings of the W-+/- to the light quarks. The observed electron and positron yields were used to estimate W-+/- boson production cross sections for the e(+/-) channels of sigma(pp -> W+X) X BR(W+ -> e(+) nu(e)) = 144.1 +/- 21.2(stat)(-10.3)(+3.4)(syst) +/- 21.6(norm) pb, and sigma(pp -> W-X) X BR(W- -> e(-) (nu) over bar (e)) = 3.17 +/- 12.1(stat)(-8.2)(+10.1)(syst) +/- 4.8(norm) pb.
14.	Adare, A, et al. (författare) Measurement of Long-Range Angular Correlation and Quadrupole Anisotropy of Pions and (Anti)Protons in Central d+Au Collisions at sqrt[s_{NN}]=200 GeV. 2015 Ingår i: Physical Review Letters. - 1079-7114. ; 114:19 Tidskriftsartikel (refereegranskat)abstract We present azimuthal angular correlations between charged hadrons and energy deposited in calorimeter towers in central d+Au and minimum bias p+p collisions at sqrt[s_{NN}]=200 GeV. The charged hadron is measured at midrapidity \|η\|<0.35, and the energy is measured at large rapidity (-3.7<η<-3.1, Au-going direction). An enhanced near-side angular correlation across \|Δη\|>2.75 is observed in d+Au collisions. Using the event plane method applied to the Au-going energy distribution, we extract the anisotropy strength v_{2} for inclusive charged hadrons at midrapidity up to p_{T}=4.5 GeV/c. We also present the measurement of v_{2} for identified π^{±} and (anti)protons in central d+Au collisions, and observe a mass-ordering pattern similar to that seen in heavy-ion collisions. These results are compared with viscous hydrodynamic calculations and measurements from p+Pb at sqrt[s_{NN}]=5.02 TeV. The magnitude of the mass ordering in d+Au is found to be smaller than that in p+Pb collisions, which may indicate smaller radial flow in lower energy d+Au collisions.
15.	Adare, A., et al. (författare) Double-spin asymmetry of electrons from heavy-flavor decays in p plus p collisions at root s=200 GeV 2013 Ingår i: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368. ; 87:1 Tidskriftsartikel (refereegranskat)abstract We report on the first measurement of the double-spin asymmetry, A(LL), of electrons from the decays of hadrons containing heavy flavor in longitudinally polarized p + p collisions at root s = 200 GeV for p(T) = 0.5 to 3.0 GeV/c. The asymmetry was measured at midrapidity (vertical bar eta vertical bar < 0.35) with the PHENIX detector at the Relativistic Heavy Ion Collider. The measured asymmetries are consistent with zero within the statistical errors. We obtained a constraint for the polarized gluon distribution in the proton of vertical bar Delta g/g(log(10)(x) = -1.6(-0.4)(+0.5), mu = m(T)(c)vertical bar(2) < 0.030 (1 sigma) based on a leading-order perturbative quantum chromodynamics model, using the measured asymmetry. DOI: 10.1103/PhysRevD.87.012011
16.	Adare, A., et al. (författare) Heavy-quark production and elliptic flow in Au plus Au collisions at root(NN)-N-S=62.4 GeV 2015 Ingår i: Physical Review C (Nuclear Physics). - 0556-2813. ; 91:4 Tidskriftsartikel (refereegranskat)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.
17.	Adare, A., et al. (författare) J/psi suppression at forward rapidity in Au plus Au collisions at root s(NN)=39 and 62.4 GeV 2012 Ingår i: Physical Review C (Nuclear Physics). - 0556-2813. ; 86:6 Tidskriftsartikel (refereegranskat)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
18.	Adare, A., et al. (författare) Charged-pion cross sections and double-helicity asymmetries in polarized p plus p collisions at root s=200 GeV 2015 Ingår i: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368. ; 91:3 Tidskriftsartikel (refereegranskat)abstract We present midrapidity charged-pion invariant cross sections, the ratio of the pi(-) to pi(+) cross sections and the charge-separated double-spin asymmetries in polarized p + p collisions at root s = p + 200 GeV. While the cross section measurements are consistent within the errors of next-to-leading-order (NLO) perturbative quantum chromodynamics predictions (pQCD), the same calculations overestimate the ratio of the charged-pion cross sections. This discrepancy arises from the cancellation of the substantial systematic errors associated with the NLO-pQCD predictions in the ratio and highlights the constraints these data will place on flavor-dependent pion fragmentation functions. The charge-separated pion asymmetries presented here sample an x range of similar to 0.03-0.16 and provide unique information on the sign of the gluon-helicity distribution.
19.	Adare, A., et al. (författare) Inclusive double-helicity asymmetries in neutral-pion and eta-meson production in + collisions at root s=200 GeV 2014 Ingår i: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368. ; 90:1 Tidskriftsartikel (refereegranskat)abstract Results are presented from data recorded in 2009 by the PHENIX experiment at the Relativistic Heavy Ion Collider for the double-longitudinal spin asymmetry, A(LL), for pi(0) and eta production in root s = 200 GeV polarized p + p collisions. Comparison of the pi(0) results with different theory expectations based on fits of other published data showed a preference for small positive values of gluon polarization, Delta G, in the proton in the probed Bjorken x range. The effect of adding the new 2009 pi(0) data to a recent global analysis of polarized scattering data is also shown, resulting in a best fit Delta G(DSSV)([0.05,0.2]) = 0.06(-0.15)(+0.11) in the range 0.05 < x < 0.2, with the uncertainty at Delta chi(2) = 9 when considering only statistical experimental uncertainties. Shifting the PHENIX data points by their systematic uncertainty leads to a variation of the best-fit value of Delta G(DSSV)([0.05,0.2]) between 0.02 and 0.12, demonstrating the need for full treatment of the experimental systematic uncertainties in future global analyses.
20.	Notarangelo, LD, et al. (författare) CD40lbase: a database of CD40L gene mutations causing X-linked hyper-IgM syndrome 1996 Ingår i: Immunology today. - 0167-5699. ; 17:11, s. 511-516 Tidskriftsartikel (refereegranskat)
21.	de Witte, T, et al. (författare) Haematopoietic stem cell transplantation for patients with myelo-dysplastic syndromes and secondary acute myeloid leukaemias: a report on behalf of the Chronic Leukaemia Working Party of the European Group for Blood and Marrow Transplantation (EBMT) 2000 Ingår i: British journal of haematology. - : Wiley. - 0007-1048. ; 110:3, s. 620-630 Tidskriftsartikel (refereegranskat)
22.	Kampfraath, A. A., et al. (författare) Genome expansion of an obligate parthenogenesis-associated Wolbachia poses an exception to the symbiont reduction model 2019 Ingår i: BMC Genomics. - : BMC. - 1471-2164. ; 20 Tidskriftsartikel (refereegranskat)abstract Background: Theory predicts that dependency within host-endosymbiont interactions results in endosymbiont genome size reduction. Unexpectedly, the largest Wolbachia genome was found in the obligate, parthenogenesis-associated wFol. In this study, we investigate possible processes underlying this genome expansion by comparing a re-annotated wFol genome to other Wolbachia genomes. In addition, we also search for candidate genes related to parthenogenesis induction (PI).Results: Within wFol, we found five phage WO regions representing 25.4% of the complete genome, few pseudogenized genes, and an expansion of DNA-repair genes in comparison to other Wolbachia. These signs of genome conservation were mirrored in the wFol host, the springtail F. candida, which also had an expanded DNA-repair gene family and many horizontally transferred genes. Across all Wolbachia genomes, there was a strong correlation between gene numbers of Wolbachia strains and their hosts. In order to identify genes with a potential link to PI, we assembled the genome of an additional PI strain, wLcla. Comparisons between four PI Wolbachia, including wFol and wLcla, and fourteen non-PI Wolbachia yielded a small set of potential candidate genes for further investigation.Conclusions: The strong similarities in genome content of wFol and its host, as well as the correlation between host and Wolbachia gene numbers suggest that there may be some form of convergent evolution between endosymbiont and host genomes. If such convergent evolution would be strong enough to overcome the evolutionary forces causing genome reduction, it would enable expanded genomes within long-term obligate endosymbionts.
23.	Hassan, M, et al. (författare) Busulphan kinetics and limited sampling model in children with leukemia and inherited disorders 1996 Ingår i: Bone marrow transplantation. - 0268-3369. ; 18:5, s. 843-850 Tidskriftsartikel (refereegranskat)
24.	Ringden, O, et al. (författare) Transplantation of peripheral blood stem cells as compared with bone marrow from HLA-identical siblings in adult patients with acute myeloid leukemia and acute lymphoblastic leukemia 2002 Ingår i: Journal of clinical oncology : official journal of the American Society of Clinical Oncology. - 0732-183X. ; 30:6, s. 136-136 Tidskriftsartikel (refereegranskat)
25.	Ringden, O, et al. (författare) Transplantation of peripheral blood stem cells as compared with bone marrow from HLA-identical siblings in patients with acute myeloid leukemia and acute lymphoblastic leukemia. 2001 Ingår i: BLOOD. - 0006-4971. ; 98:11, s. 482A-482A Konferensbidrag (övrigt vetenskapligt/konstnärligt)
26.	van den Eede, G, et al. (författare) The relevance of gene transfer to the safety of food and feed derived from genetically modified (GM) plants 2004 Ingår i: Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association. - : Elsevier BV. - 0278-6915. ; 42:7, s. 1127-1156 Tidskriftsartikel (refereegranskat)
27.	Brinkman, D. M., et al. (författare) Autologous stem cell transplantation in children with severe progressive systemic or polyarticular juvenile idiopathic arthritis: long-term follow-up of a prospective clinical trial 2007 Ingår i: Arthritis Rheum. - : Wiley. - 0004-3591. ; 56:7, s. 2410-21 Tidskriftsartikel (refereegranskat)abstract OBJECTIVE: To assess the safety and efficacy of intensive immunosuppression followed by T cell-depleted autologous hematopoietic stem cell transplantation (ASCT) for induction of disease remission in children with refractory progressive juvenile idiopathic arthritis (JIA). METHODS: Twenty-two patients with progressive refractory JIA were followed up over a median period of 80 months after pretreatment with intensive immunosuppression followed by ASCT in a multicenter, prospective, phase II clinical trial. Hematopoietic stem cells were harvested from the patients' bone marrow, depleted of T cells, and kept frozen until used for ASCT. Pretreatment of patients consisted of a combination of antithymocyte globulin, cyclophosphamide, and low-dose total body irradiation. Patients were followed up for ASCT-related complications, recovery of hematologic and immune system parameters, and disease outcomes. RESULTS: Reconstitution of hematologic values to normal range was rapid. Recovery of immune system parameters, especially normalization of CD4+, CD45RA+ naive T cells, was delayed, occurring at >/=6 months after ASCT. The prolonged period of immune deficiency resulted in a large number of viral infections and may have contributed to the development of macrophage activation syndrome (MAS), leading to death, in 2 patients. After ASCT, 8 of the 20 evaluable patients reached complete clinical remission of their JIA, 7 were partial responders, and 5 experienced a relapse of their disease (occurring 7 years after ASCT in 1 patient). Later during followup, 2 of the patients whose disease relapsed died from infections that developed after restarting immunosuppressive medication. CONCLUSION: Intensive immunosuppression followed by ASCT resulted in sustained complete remission or marked improvement in 15 of 22 patients with progressive refractory JIA. The procedure, however, is associated with significant morbidity and risk of mortality due to prolonged and severe depression of T cell immunity. After fatal complications due to MAS were observed in some patients, the protocol was amended in 1999, to ensure less profound depletion of T cells, better control of systemic disease before transplantation, antiviral prophylaxis after transplantation, and slow tapering of corticosteroids. Following these protocol modifications, no additional ASCT-related deaths were observed among the 11 patients who received the modified treatment.
28.	Cocco, Arianna, et al. (författare) Characterization of the gamma-aminobutyric acid signaling system in the zebrafish (danio rerio hamilton) central nervous system by reverse transcription-quantitative polymerase chain reaction 2017 Ingår i: Neuroscience. - : Elsevier BV. - 0306-4522 .- 1873-7544. ; 343, s. 300-321 Tidskriftsartikel (refereegranskat)abstract In the vertebrate brain, inhibition is largely mediated by raminobutyric acid (GABA). This neurotransmitter comprises a signaling machinery of GABA(A), GABA(B) receptors, transporters, glutamate decarboxylases (gads) and 4-aminobutyrate aminotransferase (abat), and associated proteins. Chloride is intimately related to GABAA receptor conductance, GABA uptake, and GADs activity. The response of target neurons to GABA stimuli is shaped by chloride-cation co-transporters (CCCs), which strictly control Cl- gradient across plasma membranes. This research profiled the expression of forty genes involved in GABA signaling in the zebrafish (Danio rerio) brain, grouped brain regions and retinas. Primer pairs were developed for reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The mRNA levels of the zebrafish GABA system share similarities with that of mammals, and confirm previous studies in non-mammalian species. Proposed GABAA receptors are alpha(1)beta(2)gamma(2), alpha(1)beta(2)delta, alpha(2b)beta(3), alpha(2b)beta(3)delta, alpha(4)beta(2)gamma(2), alpha(4)beta(2)gamma, alpha(6b)beta(2)gamma(2) and alpha(6b)beta(2)delta. Regional brain differences were documented. Retinal hetero- or homomeric rho-composed GABAA receptors could exist, accompanying alpha(1)beta(y)gamma(2), alpha(1)beta(y)delta, alpha(6a)beta(y)gamma(2,) alpha(6a)beta(y)delta. Expression patterns of alpha(6a) and alpha(6b) were opposite, with the former being more abundant in retinas, the latter in brains. Given the stoichiometry alpha(6w)beta(y)gamma(z), alpha(6a-) or alpha(6b)-containing receptors likely have different regulatory mechanisms. Different gene isoforms could originate after the rounds of genome duplication during teleost evolution. This research depicts that one isoform is generally more abundantly expressed than the other. Such observations also apply to GABAB receptors, GABA transporters, GABA-related enzymes, CCCs and GABAA receptor associated proteins, whose presence further strengthens the proof of a GABA system in zebrafish.
29.	Complementary Proceedings of the 9th Workshop on Transformation & Engineering of Enterprises, the 2nd International Workshop on Capability-oriented Business Informatics, and the 2nd Workshop on Cross-Organizational and Cross-Company BPM 2015 Proceedings (redaktörskap) (refereegranskat)
30.	Gabriëls, Suzan H E J, et al. (författare) An NB-LRR protein required for HR signalling mediated by both extra- and intracellular resistance proteins. 2007 Ingår i: Plant J. - 0960-7412 .- 1365-313X. ; 50:1, s. 14-28 Tidskriftsartikel (refereegranskat)
31.	Nikopoulou, C, et al. (författare) Spatial and single-cell profiling of the metabolome, transcriptome and epigenome of the aging mouse liver 2023 Ingår i: Nature aging. - 2662-8465. ; 3:11, s. 1430-1445 Tidskriftsartikel (refereegranskat)
32.	Nikopoulou, C, et al. (författare) Spatial and single-cell profiling of the metabolome, transcriptome and epigenome of the aging mouse liver 2023 Ingår i: Nature aging. - 2662-8465. ; 3:11, s. 1430-1445 Tidskriftsartikel (refereegranskat)
33.	Pabinger, I, et al. (författare) Mortality and Inherited Thrombophilia: results from the European Prospective Cohort on Thrombophilia (EPCOT). 2012 Ingår i: Journal of Thrombosis and Haemostasis. - : Elsevier BV. - 1538-7933 .- 1538-7836. ; 10:2, s. 217-222 Tidskriftsartikel (refereegranskat)abstract Background: Data on the survival of individuals with hereditary thrombophilia are rare and only come from retrospective studies. Objective: We aimed to assess mortality in individuals with known thrombophilia with and without a history of thrombosis in comparison to a control group. Patients/Methods: The European Prospective Cohort on Thrombophilia (EPCOT) study is a prospective multi-centre observational study performed to assess the risk of thrombosis in persons with inherited thrombophilia. In an extension of this study the vital status was assessed in 1,240 individuals with thrombophilia (mean age 40.9 years, 59% women, 196 with antithrombin-, 341 with protein C-, 276 with protein S-deficiency, 330 with factor V Leiden and 97 with combined defects, 62% with a VT history) and 875 controls (mean age 42.5 years, 48% women, 7% with a VT history). Results: Seventy-two individuals with thrombophilia and 45 controls died during follow-up. The risk of death, adjusted for sex, thrombosis-history and centre, was not associated with thrombophilia (hazard ratio (HR) thrombophilia individuals versus controls: 1.09, 95% confidence interval (CI) 0.66-1.78). When individuals with thrombophilia were evaluated separately, a history of thrombosis was not associated with mortality: the risk of death after adjustment for sex, anticoagulation and center was HR 0.79 (95% CI 0.41-1.54). Conclusions: No increased risk of death in individuals with thrombophilia, not even in those with a history of thrombosis, was observed.
34.	Passweg, JR, et al. (författare) Influence of protective isolation on outcome of allogeneic bone marrow transplantation for leukemia 1998 Ingår i: Bone marrow transplantation. - : Springer Science and Business Media LLC. - 0268-3369 .- 1476-5365. ; 21:12, s. 1231-1238 Tidskriftsartikel (refereegranskat)
35.	Tsekrekos, A., et al. (författare) Improved survival after laparoscopic compared to open gastrectomy for advanced gastric cancer: a Swedish population-based cohort study 2023 Ingår i: Gastric Cancer. - : Springer Science and Business Media LLC. - 1436-3291 .- 1436-3305. ; 26, s. 467-477 Tidskriftsartikel (refereegranskat)abstract BackgroundLaparoscopic gastrectomy is increasingly used for the treatment of locally advanced gastric cancer but concerns remain whether similar results can be obtained compared to open gastrectomy, especially in Western populations. This study compared the short-term postoperative, oncological and survival outcomes following laparoscopic versus open gastrectomy based on data from the Swedish National Register for Esophageal and Gastric Cancer.MethodsPatients who underwent surgery with curative intent for adenocarcinoma of the stomach or gastroesophageal junction Siewert type III from 2015 to 2020 were identified, and 622 patients with cT2-4aN0-3M0 tumors were included. The impact of surgical approach on short-term outcomes was assessed using multivariable logistic regression. Long-term survival was compared using multivariable Cox regression.ResultsIn total, 350 patients underwent open and 272 laparoscopic gastrectomy, of which 12.9% were converted to open surgery. The groups were similar regarding distribution of clinical disease stage (27.6% stage I, 46.0% stage II, and 26.4% stage III). Neoadjuvant chemotherapy was administered to 52.7% of the patients. There was no difference in the rate of postoperative complications, but laparoscopic approach was associated with lower 90 day mortality (1.8 vs 4.9%, p = 0.043). The median number of resected lymph nodes was higher after laparoscopic surgery (32 vs 26, p < 0.001), while no difference was found in the rate of tumor-free resection margins. Better overall survival was observed after laparoscopic gastrectomy (HR 0.63, p < 0.001).ConclusionsLaparoscopic gastrectomy can be safely preformed for advanced gastric cancer and is associated with improved overall survival compared to open surgery.
36.	Vossen, Jack, H., et al. (författare) Identification of tomato phosphatidylinositol-specific phospholipase-C (PI-PLC) family members and the role of PLC4 and PLC6 in HR and disease resistance 2010 Ingår i: The Plant Journal. - 0960-7412 .- 1365-313X. ; 62:2, s. 224-239 Tidskriftsartikel (refereegranskat)abstract The perception of pathogen-derived elicitors by plants has been suggested to involve phosphatidylinositol-specific phospholipase-C (PI-PLC) signalling. Here we show that PLC isoforms are required for the hypersensitive response (HR) and disease resistance. We characterised the tomato [Solanum lycopersicum (Sl)] PLC gene family. Six Sl PLC-encoding cDNAs were isolated and their expression in response to infection with the pathogenic fungus Cladosporium fulvum was studied. We found significant regulation at the transcriptional level of the various SlPLCs, and SlPLC4 and SlPLC6 showed distinct expression patterns in C. fulvum-resistant Cf-4 tomato. We produced the encoded proteins in Escherichia coli and found that both genes encode catalytically active PI-PLCs. To test the requirement of these Sl PLCs for full Cf-4-mediated recognition of the effector Avr4, we knocked down the expression of the encoding genes by virus-induced gene silencing. Silencing of SlPLC4 impaired the Avr4/Cf-4-induced HR and resulted in increased colonisation of Cf-4 plants by C. fulvum expressing Avr4. Furthermore, expression of the gene in Nicotiana benthamiana enhanced the Avr4/Cf-4-induced HR. Silencing of SlPLC6 did not affect HR, whereas it caused increased colonisation of Cf-4 plants by the fungus. Interestingly, Sl PLC6, but not Sl PLC4, was also required for resistance to Verticillium dahliae, mediated by the transmembrane Ve1 resistance protein, and to Pseudomonas syringae, mediated by the intracellular Pto/Prf resistance protein couple. We conclude that there is a differential requirement of PLC isoforms for the plant immune response and that Sl PLC4 is specifically required for Cf-4 function, while Sl PLC6 may be a more general component of resistance protein signalling.

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