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Kinase fusions are considered oncogenic drivers in numerous types of cancer. In lung adenocarcinoma 5–10% of patients harbor kinase fusions. The most frequently detected kinase fusion involves the Anaplastic Lymphoma Kinase (ALK) and Echinoderm Microtubule-associated protein-Like 4 (EML4). In addition, oncogenic kinase fusions involving the tyrosine kinases RET and ROS1 are found in smaller subsets of patients. In this study, we employed quantitative mass spectrometry-based phosphoproteomics to define the cellular tyrosine phosphorylation patterns induced by different oncogenic kinase fusions identified in patients with lung adenocarcinoma. We show that exogenous expression of the kinase fusions in HEK 293T cells leads to widespread tyrosine phosphorylation. Direct comparison of different kinase fusions demonstrates that the kinase part and not the fusion partner primarily defines the phosphorylation pattern. The tyrosine phosphorylation patterns differed between ALK, ROS1, and RET fusions, suggesting that oncogenic signaling induced by these kinases involves the modulation of different cellular processes.
Charmonium production in heavy ion collisions is considered as an important diagnostic probe for studying the phase diagram of strongly interacting matter for potential phase transitions. The interpretation of existing data from the CERN SPS is hampered by a lack of knowledge on the properties of open charm particle production in the fireball. Moreover, open charm production in heavy ion collisions by itself is poorly understood. To overcome this obstacle, the NA61/SHINE was equipped with a Small Acceptance Vertex Detector (SAVD), which is predicted to make the experiment sensitive to open charm mesons produced in A-A collisions at the SPS top energy. This paper will introduce the concept and the hardware of the SAVD. Moreover, first running experience as obtained in a commissioning run with a 150 AGeV/c Pb+Pb collision system will be reported.
In March 2019 the HADES experiment recorded 14 billion Ag+Ag collisions at √sNN = 2.55 GeV as a part of the FAIR phase-0 physics program. In this contribution, we present and investigate our capabilities to reconstruct and analyze weakly decaying strange hadrons and hypernuclei emerging from these collisions. The focus is put on measuring the mean lifetimes of these particles.
The multi-strange baryon yields in Pb--Pb collisions have been shown to exhibit an enhancement relative to pp reactions. In this work, Ξ and Ω production rates have been measured with the ALICE experiment as a function of transverse momentum, pT, in p-Pb collisions at a centre-of-mass energy of sNN−−−√ = 5.02 TeV. The results cover the kinematic ranges 0.6 GeV/c<pT<7.2 GeV/c and 0.8 GeV/c<pT< 5 GeV/c, for Ξ and Ω respectively, in the common rapidity interval -0.5 <yCMS< 0. Multi-strange baryons have been identified by reconstructing their weak decays into charged particles. The pT spectra are analysed as a function of event charged-particle multiplicity, which in p-Pb collisions ranges over one order of magnitude and lies between those observed in pp and Pb-Pb collisions. The measured pT distributions are compared to the expectations from a Blast-Wave model. The parameters which describe the production of lighter hadron species also describe the hyperon spectra in high multiplicity p-Pb. The yield of hyperons relative to charged pions is studied and compared with results from pp and Pb-Pb collisions. A statistical model is employed, which describes the change in the ratios with volume using a canonical suppression mechanism, in which the small volume causes a species-dependent relative reduction of hadron production. The calculations, in which the magnitude of the effect depends on the strangeness content, show good qualitative agreement with the data.
PURPOSE: This study investigates the distortion of geometry of catheters and anatomy in acquired U/S images, caused by utilizing various stand-off materials for covering a transrectal bi-planar ultrasound probe in HDR and LDR prostate brachytherapy, biopsy and other interventional procedures. Furthermore, an evaluation of currently established water-bath based quality assurance (QA) procedures is presented.
MATERIAL AND METHODS: Image acquisitions of an ultrasound QA setup were carried out at 5 MHz and 7 MHz. The U/S probe was covered by EA 4015 Silicone Standoff kit, or UA0059 Endocavity balloon filled either with water or one of the following: 40 ml of Endosgel(®), Instillagel(®), Ultraschall gel or Space OAR™ gel. The differences between images were recorded. Consequently, the dosimetric impact of the observed image distortion was investigated, using a tissue equivalent ultrasound prostate phantom - Model number 053 (CIRS Inc., Norfolk, VA, USA).
RESULTS: By using the EA 4015 Silicone Standoff kit in normal water with sound speed of 1525 m/s, a 3 mm needle shift was observed. The expansion of objects appeared in radial direction. The shift deforms also the PTV (prostate in our case) and other organs at risk (OARs) in the same way leading to overestimation of volume and underestimation of the dose. On the other hand, Instillagel(®) and Space OAR™ "shrinks" objects in an ultrasound image for 0.65 mm and 0.40 mm, respectively.
CONCLUSIONS: The use of EA 4015 Silicone Standoff kit for image acquisition, leads to erroneous contouring of PTV and OARs and reconstruction and placement of catheters, which results to incorrect dose calculation during prostate brachytherapy. Moreover, the reliability of QA procedures lies mostly in the right temperature of the water used for accurate simulation of real conditions of transrectal ultrasound imaging.
Background: In the context of the investigation of the quark gluon plasma produced in heavy-ion collisions, hadrons containing heavy (charm or beauty) quarks play a special role for the characterization of the hot and dense medium created in the interaction. The measurement of the production of charm and beauty hadrons in proton–proton collisions, besides providing the necessary reference for the studies in heavy-ion reactions, constitutes an important test of perturbative quantum chromodynamics (pQCD) calculations. Heavy-flavor production in proton–nucleus collisions is sensitive to the various effects related to the presence of nuclei in the colliding system, commonly denoted cold-nuclear-matter effects. Most of these effects are expected to modify open-charm production at low transverse momenta (pT) and, so far, no measurement of D-meson production down to zero transverse momentum was available at mid-rapidity at the energies attained at the CERN Large Hadron Collider (LHC).
Purpose: The measurements of the production cross sections of promptly produced charmed mesons in p-Pb collisions at the LHC down to pT=0 and the comparison to the results from pp interactions are aimed at the assessment of cold-nuclear-matter effects on open-charm production, which is crucial for the interpretation of the results from Pb-Pb collisions.
Methods: The prompt charmed mesons D0,D+,D*+, and D+s were measured at mid-rapidity in p-Pb collisions at a center-of-mass energy per nucleon pair √sNN=5.02 TeV with the ALICE detector at the LHC. D mesons were reconstructed from their decays D0→K−π+,D+→K−π+π+, D*+→D0π+,D+s→ϕπ+→K−K+π+, and their charge conjugates, using an analysis method based on the selection of decay topologies displaced from the interaction vertex. In addition, the prompt D0 production cross section was measured in pp collisions at √s=7 TeV and p-Pb collisions at √sNN=5.02 TeV down to pT=0 using an analysis technique that is based on the estimation and subtraction of the combinatorial background, without reconstruction of the D0 decay vertex.
Results: The production cross section in pp collisions is described within uncertainties by different implementations of pQCD calculations down to pT=0. This allowed also a determination of the total c¯c production cross section in pp collisions, which is more precise than previous ALICE measurements because it is not affected by uncertainties owing to the extrapolation to pT=0. The nuclear modification factor RpPb(pT), defined as the ratio of the pT-differential D meson cross section in p-Pb collisions and that in pp collisions scaled by the mass number of the Pb nucleus, was calculated for the four D-meson species and found to be compatible with unity within uncertainties. The results are compared to theoretical calculations that include cold-nuclear-matter effects and to transport model calculations incorporating the interactions of charm quarks with an expanding deconfined medium.
Conclusions: These measurements add experimental evidence that the modification of the D-meson transverse momentum distributions observed in Pb–Pb collisions with respect to pp interactions is due to strong final-state effects induced by the interactions of the charm quarks with the hot and dense partonic medium created in ultrarelativistic heavy-ion collisions. The current precision of the measurement does not allow us to draw conclusions on the role of the different cold-nuclear-matter effects and on the possible presence of additional hot-medium effects in p-Pb collisions. However, the analysis technique without decay-vertex reconstruction, applied on future larger data samples, should provide access to the physics-rich range down to pT=0.
The production cross sections of the prompt charmed mesons D0, D+, D∗+ and Ds were measured at mid-rapidity in p-Pb collisions at a centre-of-mass energy per nucleon pair sNN−−−√=5.02 TeV with the ALICE detector at the LHC. D mesons were reconstructed from their decays D0→K−π+, D+→K−π+π+, D∗+→D0π+, D+s→ϕπ+→K−K+π+, and their charge conjugates. The pT-differential production cross sections were measured at mid-rapidity in the interval 1<pT<24 GeV/c for D0, D+ and D∗+ mesons and in 2<pT<12 GeV/c for Ds mesons, using an analysis method based on the selection of decay topologies displaced from the interaction vertex. The production cross sections of the D0, D+ and D∗+ mesons were also measured in three pT intervals as a function of the rapidity ycms in the centre-of-mass system in −1.26<ycms<0.34. In addition, the prompt D0 cross section was measured in pp collisions at s√=7 TeV and p-Pb collisions at sNN−−−√=5.02 TeV down to pT=0 using an analysis technique that is based on the estimation and subtraction of the combinatorial background, without reconstruction of the D0 decay vertex. The nuclear modification factor RpPb(pT), defined as the ratio of the pT-differential D-meson cross section in p-Pb collisions and that in pp collisions scaled by the mass number of the Pb nucleus, was calculated for the four D-meson species and found to be compatible with unity within experimental uncertainties. The results are compared to theoretical calculations that include cold-nuclear-matter effects and to transport model calculations incorporating the interactions of charm quarks with an expanding deconfined medium.
The production cross sections of the prompt charmed mesons D0, D+, D∗+ and Ds were measured at mid-rapidity in p-Pb collisions at a centre-of-mass energy per nucleon pair sNN−−−√=5.02 TeV with the ALICE detector at the LHC. D mesons were reconstructed from their decays D0→K−π+, D+→K−π+π+, D∗+→D0π+, D+s→ϕπ+→K−K+π+, and their charge conjugates. The pT-differential production cross sections were measured at mid-rapidity in the interval 1<pT<24 GeV/c for D0, D+ and D∗+ mesons and in 2<pT<12 GeV/c for Ds mesons, using an analysis method based on the selection of decay topologies displaced from the interaction vertex. The production cross sections of the D0, D+ and D∗+ mesons were also measured in three pT intervals as a function of the rapidity ycms in the centre-of-mass system in −1.26<ycms<0.34. In addition, the prompt D0 cross section was measured in pp collisions at s√=7 TeV and p-Pb collisions at sNN−−−√=5.02 TeV down to pT=0 using an analysis technique that is based on the estimation and subtraction of the combinatorial background, without reconstruction of the D0 decay vertex. The nuclear modification factor RpPb(pT), defined as the ratio of the pT-differential D-meson cross section in p-Pb collisions and that in pp collisions scaled by the mass number of the Pb nucleus, was calculated for the four D-meson species and found to be compatible with unity within experimental uncertainties. The results are compared to theoretical calculations that include cold-nuclear-matter effects and to transport model calculations incorporating the interactions of charm quarks with an expanding deconfined medium.
The measurement of prompt D-meson production as a function of multiplicity in p-Pb collisions at sNN−−−√=5.02 TeV with the ALICE detector at the LHC is reported. D0, D+ and D∗+ mesons are reconstructed via their hadronic decay channels in the centre-of-mass rapidity range −0.96<ycms<0.04 and transverse momentum interval 1<pT<24 GeV/c. The multiplicity dependence of D-meson production is examined by either comparing yields in p-Pb collisions in different event classes, selected based on the multiplicity of produced particles or zero-degree energy, with those in pp collisions, scaled by the number of binary nucleon-nucleon collisions (nuclear modification factor); as well as by evaluating the per-event yields in p-Pb collisions in different multiplicity intervals normalised to the multiplicity-integrated ones (relative yields). The nuclear modification factors for D0, D+ and D∗+ are consistent with one another. The D-meson nuclear modification factors as a function of the zero-degree energy are consistent with unity within uncertainties in the measured pT regions and event classes. The relative D-meson yields, calculated in various pT intervals, increase as a function of the charged-particle multiplicity. The results are compared with the equivalent pp measurements at s√=7 TeV as well as with EPOS~3 calculations.