| 1. |
- 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
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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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| 2. |
- Tardocchi, M., et al.
(författare)
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Modeling of neutron emission spectroscopy in JET discharges with fast tritons from (T)D ion cyclotron heating
- 2006
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Ingår i: Review of Scientific Instruments. - : AIP Publishing. - 0034-6748 .- 1089-7623. ; 77:12
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Tidskriftsartikel (refereegranskat)abstract
- The measurement of fast ion populations is one of the diagnostic capabilities provided by neutron emission spectroscopy (NES). NES measurements were carried out during JET trace tritium campaign with the magnetic proton recoil neutron spectrometer. A favorable plasma scenario is (T)D where the resulting 14 MeV neutron yield is dominated by suprathermal emission from energetic tritons accelerated by radio frequency at their fundamental cyclotron frequency. Information on the triton distribution function has been derived from NES data with a simple model based on two components referred to as bulk (B) and high energy (HE). The HE component is based on strongly anisotropic tritium distribution that can be used for routine best-fit analysis to provide tail temperature values (T-HE). This article addresses to what extent the T-HE values are model dependent by comparing the model above with a two-temperature (bi-) Maxwellian model featuring parallel and perpendicular temperatures. The bi-Maxwellian model is strongly anisotropic and frequently used for radio frequency theory.
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| 3. |
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| 4. |
- Andersson Sundén, Erik, et al.
(författare)
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The thin-foil magnetic proton recoil neutron spectrometer MPRu at JET
- 2009
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 610:3, s. 682-699
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Tidskriftsartikel (refereegranskat)abstract
- Neutrons are produced in fusion energy experiments with both deuterium (D) and deuterium–tritium (DT) plasmas. Neutron spectroscopy is a valuable tool in the study of the underlying fuel ion populations. The magnetic proton recoil neutron spectrometer, originally installed at JET in 1996 for 14-MeV neutron measurements, has been upgraded, with the main aim of improving its signal-to-background ratio (S/B), making measurements of the 2.5-MeV neutron emission in D plasmas possible. The upgrade includes a new focal-plane detector, based on the phoswich technique and consequently less sensitive to background, and a new custom-designed digital data acquisition system based on transient recorder cards. Results from JET show that the upgraded MPRu can measure 2.5-MeV neutrons with S/B=5, an improvement by a factor of 50 compared with the original MPR. S/B of 2.8×104 in future DT experiments is estimated. The performance of the MPRu is exemplified with results from recent D plasma operations at JET, concerning both measurements with Ohmic, ion cyclotron resonance (ICRH) and neutral beam injection (NBI) plasma heating, as well as measurements of tritium burn-up neutrons. The upgraded instrument allows for 2.5-MeV neutron emission and deuterium ion temperature measurements in plasmas with low levels of tritium, a feature necessary for the ITER experiment.
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| 5. |
- Conroy, Sean W., et al.
(författare)
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Neutron spectrometer for ITER using silicon detectors
- 2008
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Ingår i: Review of Scientific Instruments. - : AIP Publishing. - 0034-6748 .- 1089-7623. ; 79:10, s. 10E508-
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Tidskriftsartikel (refereegranskat)abstract
- High resolution neutron spectrometers provide information about plasma parameters at existing fusion experiments. Such a system may also be employed at ITER. Proton recoil telescopes have classically been used to detect neutrons with good energy resolution but poor efficiency. Using annular silicon detectors, it is possible to greatly increase the solid angle coverage and hence improve efficiency. Based on a simulation (MCNPX) study, the scaling of energy resolution, efficiency, and time to determine an ion temperature to 10% accuracy on foil thickness and detector location is shown. The latter quantity is used to determine the optimum foil thickness and detector geometry for specific plasma temperatures. For a 20 keV deuterium-tritium (DT) plasma, 5.3% resolution with efficiency of 2.9x10(-4) n cm(2) is attainable using the available detectors. This gives a temperature measurement with 10% accuracy in 1.1 ms for a neutron flux of 2x10(9) n cm(-2). Multiple detectors can be used to further increase the efficiency if needed. A system of this kind could be tested in a future DT campaign at, for example, JET.
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| 6. |
- Elsik, Christine G., et al.
(författare)
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The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution
- 2009
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528
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Tidskriftsartikel (refereegranskat)abstract
- To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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| 7. |
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| 8. |
- Gatu Johnson, Maria, et al.
(författare)
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The 2.5-MeV neutron time-of-flight spectrometer TOFOR for experiments at JET
- 2008
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 591:2, s. 417-430
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Tidskriftsartikel (refereegranskat)abstract
- A time-of-flight (TOF) spectrometer for measurement of the 2.5-MeV neutron emission from fusion plasmas has been developed and put into use at the JET tokamak. It has been optimized for operation at high rates (TOFOR) for the purpose of performing advanced neutron emission spectroscopy (NES) diagnosis of deuterium plasmas with a focus on the fuel ion motional states for different auxiliary heating scenarios. This requires operation over a large dynamic range, including high rates of > 100 kHz with a maximum value of 0.5 MHz for the TOFOR design. This paper describes the design principles and their technical realization. The performance is illustrated with recent neutron TOF spectra recorded for plasmas subjected to different heating scenarios. A true event count rate of 39 kHz has been achieved at about a tenth of the expected neutron yield limit of JET, giving a projected maximum of 400 kHz at peak JET plasma yield. This means that the count rate capability for NES diagnosis of D plasmas has been improved more than an order of magnitude. Another important performance factor is the spectrometer bandwidth, where data have been acquired and analyzed successfully with a response function for neutrons over the energy range 1 to > 5 MeV. The implications of instrumental advancement represented by TOFOR are discussed.
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| 9. |
- Gatu Johnson, Maria, 1978-, et al.
(författare)
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The TOFOR neutron spectrometer and its first use at JET
- 2006
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Ingår i: Review of Scientific Instruments. - American Institute of Physics : AIP Publishing. - 0034-6748 .- 1089-7623. ; 77:10E702, s. 1-3
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Tidskriftsartikel (refereegranskat)abstract
- A time-of-flight neutron spectrometer (TOFOR) has been developed to measure the 2.45 MeV d+d3He+n neutron emission from D plasmas. The TOFOR design features the capability to operate at high rates in the 100 kHz range, data collection with fast time digitizing and storing, and monitoring of the signals from the scintillation detectors used. This article describes the principles of the instrument and its installation at JET and presents preliminary data to illustrate the TOFOR performance as a neutron emission spectroscopy diagnostic.
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| 10. |
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| 11. |
- Giacomelli, Luca, et al.
(författare)
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Advanced Neutron Diagnostics for JET and ITER Fusion Experiments
- 2005
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 45, s. 1191-1201
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Tidskriftsartikel (refereegranskat)abstract
- The diagnostics functions of neutron measurements as well as the roles played by neutron yield monitors, cameras and spectrometers are reviewed. The importance of recent developments in neutron emission spectroscopy (NES) diagnostics is emphasized. Results are presented from the NES diagnosis of the Joint European Torus (JET) plasmas performed with the magnetic proton recoil (MPR) spectrometer during the first deuterium tritium experiment of 1997 and the recent trace tritium experiment of 2003. The NES diagnostic capabilities at JET are presently being enhanced by an upgrade of the MPR (MPRu) and a new 2.5 MeV time-of-flight (TOF) neutron spectrometer (TOFOR). The principles of MPRu and TOFOR are described and illustrated with the diagnostic role they will play in the high performance fusion experiments in the forward programme of JET largely aimed at supporting the International Thermonuclear Experimental Reactor (ITER). The importance of the JET NES effort for ITER is discussed.
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| 12. |
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| 13. |
- Hellesen, Carl, et al.
(författare)
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Validation of TRANSP Simulations Using Neutron emission Spectroscopy with Dual Sight Lines
- 2008
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Ingår i: Review of Scientific Instruments. - : AIP Publishing. - 0034-6748 .- 1089-7623. ; 79:10, s. 10E510-
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Tidskriftsartikel (refereegranskat)abstract
- A method to generate modeled neutron spectra from bulk and fast ion distributions simulated by TRANSP has been developed. In this paper, modeled data generated from fuel ion distrubutions modeled with TRANSP is compared to measured data from two neutron spectrometers with different lines of sight; TOFOR with a radial one and the MPRu with a tangential one. The information obtained from the analysis of the measured neutron spectra such as the relative intensity of the emission from different ion populations places additional constraints on the simulation and can be used to adjust the parameters of the simulation.
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| 14. |
- Ronchi, Emanuele, et al.
(författare)
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A bipolar LED drive technique for high performance, stability and power in the nanosecond time scale
- 2009
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 599:2-3, s. 243-247
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Tidskriftsartikel (refereegranskat)abstract
- Pulsed light sources are often used to monitor the stability of light detectors such as photomultiplier tubes. Light emitting diodes (LEDs) are suitable for this due to their high specific light yield. While pulsed operation in the region of [mu]s is generally accessible with most LEDs and drivers, the ns time scale often represents a technical challenge. This paper describes a technique of bipolar LED drive that can produce light pulses of a few ns at high stability, reliability and power. The driver also offers control over the properties of the light pulse produced such as shape, intensity and repetition rate. This approach has been studied in 2003 and implemented in 2004 for two fusion neutron spectrometers at the Joint European Torus (JET) namely the Magnetic Proton Recoil upgrade (MPRu) and the Time Of Flight Optimized for Rate (TOFOR). A driver has been manufactured and connected to the scintillation detectors of each spectrometer through an optical fiber distribution network. Both MPRu and TOFOR have been successfully relying on this system for calibration and performance monitoring for several years, confirming the long-term stability and reliability of this technique.
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| 15. |
- Ronchi, Emanuele, 1978-, et al.
(författare)
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A neural network pulse shape discrimination and pile-up rejection framework for the BC501 neutron/gamma liquid scintillator
- 2009
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 610:2, s. 534-539
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Tidskriftsartikel (refereegranskat)abstract
- BC-501 is a liquid scintillation detector sensitive to both neutrons and gamma rays. As these produce slightly different signals in the detector, they can be discriminated based on their pulse shape (Pulse Shape Discrimination, PSD). This paper reports on results obtained with several PSD techniques and compares them with a method based on artificial neural networks (NN) developed for this application. Results indicated a large performance advantage of NN especially in the region of small deposited energy which typically contains the majority of the events. NN were also applied for discrimination of pile-up events with good results. This framework can be implemented on some of the most recent programmable data acquisition cards and it is suitable for real-time application.
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| 16. |
- Ronchi, E, et al.
(författare)
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A Neural Networks Framework for Real-Time Unfolding of Neutron Spectroscopic Data at JET
- 2008
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Ingår i: Review of Scientific Instruments. - : AIP Publishing. - 0034-6748 .- 1089-7623. ; 79:10, s. 10E513-
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Tidskriftsartikel (refereegranskat)abstract
- A determination of fast ion population parameters such as intensity and kinetic temperature is important for fusion reactors. This becomes more challenging with finer time resolution of the measurements, since the limited data in each time slice cause increasing statistical variations in the data. This paper describes a framework using Bayesian-regularized neural networks (NNs) designed for such a task. The method is applied to the TOFOR 2.5 MeV fusion neutron spectrometer at JET. NN training data are generated by random sampling of variables in neutron spectroscopy models. Ranges and probability distributions of the parameters are chosen to match the experimental data. Results have shown good performance both on synthetic and experimental data. The latter was assessed by statistical considerations and by examining the robustness and time consistency of the results. The regularization of the training algorithm allowed for higher time resolutions than simple forward methods. The fast execution time makes this approach suitable for real-time analysis with a time resolution limit in the microsecond time scale.
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| 17. |
- Ronchi, Emanuele, et al.
(författare)
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An artificial neural network based neutron-gamma discrimination and pile-up rejection framework for the BC-501 liquid scintillation detector
- 2009
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 610:2, s. 534-539
-
Tidskriftsartikel (refereegranskat)abstract
- BC-501 is a liquid scintillation detector sensitive to both neutrons and gamma rays. As these produce slightly different signals in the detector, they can be discriminated based on their pulse shape (Pulse Shape Discrimination, PSD). This paper reports on results obtained with several PSD techniques and compares them with a method based on artificial neural networks (NN) developed for this application. Results indicated a large performance advantage of NN especially in the region of small deposited energy which typically contains the majority of the events. NN were also applied for discrimination of pile-up events with good results. This framework can be implemented on some of the most recent programmable data acquisition cards and it is suitable for real-time application.
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| 18. |
- Sjöstrand, Henrik, et al.
(författare)
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Fusion Power Measurement Using a Combined Neutron Spectrometer - Camera System at ITER
- 2008
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Ingår i: BURNING PLASMA DIAGNOSTICS. - New York : American Institute of Physics (AIP). - 9780735405073 ; , s. 319-322
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Konferensbidrag (refereegranskat)abstract
- A central task for fusion plasma diagnostics is to measure the 2.5 and 14 MeV neutron emission rate in order to determine the fusion power. A new method for determining the neutron yield has been developed at JET. It makes use of the magnetic proton recoil neutron spectrometer and a neutron camera and provides the neutron yield with small systematic errors. At ITER a similar system could operate if a high-resolution, high-performance neutron spectrometer similar to the MPR was installed. In this paper, we present how such system could be implemented and how well it would perform under different assumption of plasma scenarios and diagnostic capabilities. It is found that the systematic uncertainty for using such a system as an absolute calibration reference is as low as 3 % and hence it would be an excellent candidate for the calibration of neutron monitors such as fission chambers. It is also shown that the system could provide a 1 ms time resolved estimation of the neutron rate with a total uncertainty of 5 %.
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| 19. |
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| 20. |
- Sjöstrand, Henrik, et al.
(författare)
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Gain stabilization control system of the upgraded magnetic protonrecoil neutron spectrometer at JET
- 2009
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Ingår i: Review of Scientific Instruments. - : AIP Publishing. - 0034-6748 .- 1089-7623. ; 80:6, s. 063505-
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Tidskriftsartikel (refereegranskat)abstract
- Burning plasma experiments such as ITER and DEMO require diagnostics capable of withstanding the harsh environment generated by the intense neutron flux and to maintain stable operating conditions for times longer than present day systems. For these reasons, advanced control and monitoring (CM) systems will be necessary for the reliable operation of diagnostics. This paper describes the CM system of the upgraded magnetic proton recoil neutron spectrometer installed at the Joint European Torus focusing in particular on a technique for the stabilization of the gain of the photomultipliers coupled to the neutron detectors. The results presented here show that this technique provides good results over long time scales. The technique is of general interest for all diagnostics that employ scintillators coupled to photomultiplier tubes.
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| 21. |
- Sjöstrand, Henrik, et al.
(författare)
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Gain stabilization control system of the upgraded magneticproton recoil neutron spectrometer at JET
- 2009
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Ingår i: Review of Scientific Instruments. - : AIP Publishing. - 0034-6748 .- 1089-7623. ; 80:6, s. 063505-
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Tidskriftsartikel (refereegranskat)abstract
- Burning plasma experiments such as ITER and DEMO require diagnostics capable of withstanding the harsh environment generated by the intense neutron flux and to maintain stable operating conditions for times longer than present day systems. For these reasons, advanced control and monitoring (CM) systems will be necessary forthe reliable operation of diagnostics. This paper describes the CM system of theupgraded magnetic proton recoil neutron spectrometer installed at the Joint European Torus focusing in particular on a technique for the stabilization of the gain of thephotomultipliers coupled to the neutron detectors. The results presented here show that this technique provides good results over long time scales. The technique is of general interest for all diagnostics that employ scintillators coupled to photomultiplier tubes.
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