| 1. |
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| 2. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
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| 4. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
- 2008
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In: Autophagy. - : Landes Bioscience. - 1554-8627 .- 1554-8635. ; 4:2, s. 151-175
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Research review (peer-reviewed)abstract
- Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.
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| 5. |
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| 6. |
- Le Coroller, H., et al.
(author)
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K-Stacker : an algorithm to hack the orbital parameters of planets hidden in high-contrast imaging
- 2020
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 639
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Journal article (peer-reviewed)abstract
- Context. Recent high-contrast imaging surveys, using the Spectro-Polarimetic High contrast imager for Exoplanets REsearch (SPHERE) or the Gemini Planet Imager in search of planets in young, nearby systems, have shown evidence of a small number ofgiant planets at relatively large separation beyond 10–30 au, where those surveys are the most sensitive. Access to smaller physical separations between 5 and 30 au is the next step for future planet imagers on 10 m telescopes and the next generation of extremely large telescopes in order to bridge the gap with indirect techniques such as radial velocity, transit, and soon astrometry with Gaia. In addition to new technologies and instruments, the development of innovative observing strategies combined with optimized data processing tools is participating in the improvement of detection capabilities at very close angular separation. In that context, we recently proposed a new algorithm, Keplerian-Stacker, which combines multiple observations acquired at different epochs and takes into account the orbital motion of a potential planet present in the images to boost the ultimate detection limit. We showed that this algorithm is able to find planets in time series of simulated images of the SPHERE InfraRed Dual-band Imager and Spectrograph (IRDIS) even when a planet remains undetected at one epoch.Aims. Our goal is to test and validate the K-Stacker algorithm performances on real SPHERE datasets to demonstrate the resilience of this algorithm to instrumental speckles and the gain offered in terms of true detection. This will motivate future dedicated multi-epoch observation campaigns of well-chosen, young, nearby systems and very nearby stars carefully selected to search for planets in emitted and reflected light, respectively, to open a new path concerning the observing strategy used with current and future planet imagers.Methods. To test K-Stacker, we injected fake planets and scanned the low signal-to-noise ratio (S/N) regime in a series of raw observations obtained by the SPHERE/IRDIS instrument in the course of the SPHERE High-contrast ImagiNg survey for Exoplanets. We also considered the cases of two specific targets intensively monitored during this campaign: β Pictoris and HD 95086. For each target and epoch, the data were reduced using standard angular differential imaging processing techniques and then recombined with K-Stackerto recover the fake planetary signals. In addition, the known exoplanets β Pictoris b and HD 95086 b previously identified at lower S/N in single epochs have also been recovered by K-Stacker.Results. We show that K-Stacker achieves a high success rate of ≈100% when the S/N of the planet in the stacked image reaches≈9. The improvement of the S/N is given as the square root of the total exposure time contained in the data being combined. At S/N<6−7, the number of false positives is high near the coronagraphic mask, but a chromatic study or astrophysical criteria can help to disentangle between a bright speckle and a true detection. During the blind test and the redetection of HD 95086 b, and β Pic b, we highlight the ability of K-Stacker to find orbital solutions consistent with those derived by the current Markov chain Monte Carlo orbital fitting techniques. This confirms that in addition to the detection gain, K-Stacker offers the opportunity to characterize the most probable orbital solutions of the exoplanets recovered at low S/N.
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| 7. |
- Pietri, S., et al.
(author)
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First Results from the Stopped Beam Isomer RISING Campaign at GSI
- 2007
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In: Acta Physica Polonica. Series B: Elementary Particle Physics, Nuclear Physics, Statistical Physics, Theory of Relativity, Field Theory. - 0587-4254. ; 38:4, s. 1255-1264
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Journal article (peer-reviewed)abstract
- The first results from a series of experiments focused on the study of the internal structure of nuclei at the extremes of N:Z ratio using isomer spectroscopy are reported. These experiments represent the first of the Stopped Beam section of the Rare Isotopes Investigations at GSI (RISING) project. Exotic nuclei were synthesized using relativistic projectile fragmentation of similar to 500 -> 1000 MeV/u beams of Ag-107, Pb-208, Xe-136 and Ni-58, or fission of 750 MeV/u U-238 provided by the SIS synchrotron at GSI. A detailed description of the RISING stopped beam set up is given, together with a report of the performance of the associated gamma-ray spectrometer array. Selected results of the first experimental campaign are presented together with a discussion on the use of isomeric spectroscopy to study GeV range nuclear fragmentation. Details on future research plans of this collaboration are also outlined.
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| 8. |
- Steer, S. J., et al.
(author)
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Isomeric States Observed in Heavy Neutron-rich Nuclei Populated in the Fragmentation of a 208Pb Beam
- 2011
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In: Physical Review C (Nuclear Physics). - 0556-2813. ; 84:4
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Journal article (peer-reviewed)abstract
- Heavy neutron-rich nuclei were populated via the fragmentation of a E/A = 1 GeV Pb-208(82) beam. Secondary fragments were separated and identified and subsequently implanted in a passive stopper. By the detection of delayed gamma rays, isomeric decays associated with these nuclei have been identified. A total of 49 isomers were detected, with the majority of them observed for the first time. The newly discovered isomers are in Hg-204,205(80), Au-201,202,204,205(79), Pt-197,203,204(78), Ir-195,199-203(77), Os-193,197-199(76), Re-196(75), W-190,191(74), and Ta-189(73). Possible level schemes are constructed and the structure of the nuclei discussed. To aid the interpretation, shell-model as well as BCS calculations were performed.
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| 9. |
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| 10. |
- Podolyak, Zs., et al.
(author)
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Structure of Neutron-rich Nuclei Around the N=126 Closed Shell; the Yrast Structure of 205Au up to Spin-parity I = (19/2+)
- 2009
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In: European Physical Journal A. - : Springer Science and Business Media LLC. - 1434-6001 .- 1434-601X. ; 42:3, s. 489-493
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Conference paper (peer-reviewed)abstract
- Heavy neutron-rich nuclei have been populated through the relativistic fragmentation of a Pb-208(82) beam at E/A = 1 GeV on a 2.5 g/cm(2) thick Be target. The synthesised nuclei were selected and identified in-flight using the fragment separator at GSI. Approximately 300 ns after production, the selected nuclei were implanted in an similar to 8 mm thick perspex stopper, positioned at the centre of the RISING gamma-ray detector spectrometer array. A previously unreported isomer with a half-life T-1/2 = 163(5) ns has been observed in the N = 126 closed-shell nucleus Au-205(79). Through gamma-ray singles and gamma-gamma coincidence analysis a level scheme was established. The comparison with a shell model calculation tentatively identifies the spin-parity of the excited states, including the isomer itself, which is found to be I-pi = (19/2(+)).
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| 11. |
- Regan, P. H., et al.
(author)
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First Results from the Stopped RISING Campaign at GSI: The Mapping of Isomeric Decays in Highly Exotic Nuclei
- 2007
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In: AIP Conference Proceedings. - : AIP. - 0094-243X. - 9780735413283 ; 899, s. 19-22
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Conference paper (peer-reviewed)abstract
- The first results from the Stopped Beam RISING experimental campaign performed at the GSI laboratory in Darmstadt, Germany, are presented. RISING (Rare ISotope INvestigations at GSI) constitutes a major new experimental program in European nuclear structure physics research aimed at using relativistic‐energy, projectile‐fragmentation reactions to study nuclei with exotic proton‐to‐neutron ratios. This paper introduces the physics aims of the Stopped RISING collaboration and presents some technical details and initial results from experiments using the RISING array to study decays from metastable nuclear states in both proton and neutron‐rich nuclei.
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| 12. |
- Rudolph, Dirk, et al.
(author)
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Exciting Isomers from the First Stopped-beam RISING Campaign
- 2007
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In: The European Physical Journal. Special Topics. - : Springer Science and Business Media LLC. - 1951-6355 .- 1951-6401. ; 150, s. 173-176
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Journal article (peer-reviewed)abstract
- First results are reported from a major new initiative of experiments, which focus on nuclear structure studies at extreme isospin values by means of isomer spectroscopy. The experiments represent the first part of the so-called stopped-beam campaign within the Rare ISotope INvestigations at GSI (RISING) project. Time-correlated gamma decays from individually identified nuclear species have been measured, allowing the clean identification of isomeric decays in a wide range of exotic nuclei both at the proton drip-line and in heavy, neutron-rich systems. An overview of the experimental technique will be given, together with the performance of the new germanium detector array and future research plans for the collaboration.
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| 13. |
- Steer, S. J., et al.
(author)
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Isomeric Decay Studies In Neutron-Rich N Approximate To 126 Nuclei
- 2009
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In: International Journal Of Modern Physics E-Nuclear Physics. - 0218-3013. ; 18:4, s. 1002-1007
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Conference paper (peer-reviewed)abstract
- Heavy neutron-rich nuclei were populated via relativistic energy fragmentation of a E/A= 1 GeV Pb-208 beam. The nuclei of interest were selected and identified by a fragment separator and then implanted in a passive plastic stopper. Delayed. rays following internal isomeric decays were detected by the RISING array. Experimental information was obtained on a number of nuclei with Z=73-80 (Ta-Hg), providing new information both on the prolate-oblate transitional region as well as on the N=126 closed shell nuclei.
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| 14. |
- Steer, S. J., et al.
(author)
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Single-particle Behavior at N=126: Isomeric Decays in Neutron-rich 204Pt
- 2008
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In: Physical Review C (Nuclear Physics). - 0556-2813. ; 78:6
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Journal article (peer-reviewed)abstract
- The four proton-hole nucleus Pt-204 was populated in the fragmentation of an E/A = 1 GeV Pb-208 beam. The yrast structure of Pt-204 has been observed up to angular momentum I = 10h by detecting delayed gamma-ray transitions originating from metastable states. These long-lived excited states have been identified to have spin-parities of I-pi = (10(+)), (7(-)), and (5(-)) and half-lives of T-1/2 = 146(14) ns, 55(3) mu s, and 5.5(7) mu s, respectively. The structure of the magic N = 126 Pt-204 nucleus is discussed and understood in terms of the spherical shell model. The data suggest a revision of the two-body interaction for N = 126, Z < 82, which determines the evolution of nuclear structure toward the r-process waiting point nuclei.
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| 16. |
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| 17. |
- Al-Dahan, N., et al.
(author)
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Multiple beta(-) decaying states in Re-194: Shape evolution in neutron-rich osmium isotopes
- 2012
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In: Physical Review C (Nuclear Physics). - 0556-2813. ; 85:3
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Journal article (peer-reviewed)abstract
- beta decays from heavy, neutron-rich nuclei with A similar to 190 have been investigated following their production via the relativistic projectile fragmentation of an E/A = 1 GeV Pb-208 primary beam on a similar to 2.5 g/cm(2) Be-9 target. The reaction products were separated and identified using the GSI FRagment Separator (FRS) and stopped in the RISING active stopper. gamma decays were observed and correlated with these secondary ions on an event-by-event basis such that gamma-ray transitions following from both internal (isomeric) and beta decays were recorded. A number of discrete, beta-delayed gamma-ray transitions associated with beta decays from Re-194 to excited states in Os-194 have been observed, including previously reported decays from the yrast I-pi = (6(+)) state. Three previously unreported gamma-ray transitions with energies 194, 349, and 554 keV are also identified; these transitions are associated with decays from higher spin states in Os-194. The results of these investigations are compared with theoretical predictions from Nilsson multi-quasiparticle (MQP) calculations. Based on lifetime measurements and the observed feeding pattern to states in Os-194, it is concluded that there are three beta(-)-decaying states in Re-194.
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| 18. |
- Alkhomashi, N., et al.
(author)
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Beta(-)-Delayed And Isomer Spectroscopy Of Neutron-Rich Ta And W Isotopes
- 2009
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In: Acta Physica Polonica B. - 0587-4254. ; 40:3, s. 875-878
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Conference paper (peer-reviewed)abstract
- Decays of neutron-rich A similar to 190 nuclei have been studied following projectile fragmentation of a Pb-208 beam on a Be-9 target at the GSI Fragment Separator. Gamma-ray decays from previously reported isomeric states in Ta-188, W-190 and (192,193) Re were used as internal calibrations for the particle identification analysis, together with the identification of previously unreported isomeric decays in Ta-189 and W-191. The current work also identifies beta-delayed gamma rays following the decay of Ta-188 to W-188 for the first time.
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| 19. |
- Alkhomashi, N., et al.
(author)
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beta(-)-delayed spectroscopy of neutron-rich tantalum nuclei: Shape evolution in neutron-rich tungsten isotopes
- 2009
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In: Physical Review C (Nuclear Physics). - 0556-2813. ; 80:6
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Journal article (peer-reviewed)abstract
- The low-lying structure of W-188,W-190,W-192 has been studied following beta decays of the neutron-rich mother nuclei Ta-188,Ta-190,Ta-192 produced following the projectile fragmentation of a 1-GeV-per-nucleon Pb-208 primary beam on a natural beryllium target at the GSI Fragment Separator. The beta-decay half-lives of Ta-188, Ta-190, and Ta-192 have been measured, with gamma-ray decays of low-lying states in their respective W daughter nuclei, using heavy-ion beta-gamma correlations and a position-sensitive silicon detector setup. The data provide information on the low-lying excited states in W-188, W-190, and W-192, which highlight a change in nuclear shape at W-190 compared with that of lighter W isotopes. This evolution of ground-state structure along the W isotopic chain is discussed as evidence for a possible proton subshell effect for the A similar to 190 region and is consistent with maximization of the gamma-softness of the nuclear potential around N similar to 116.
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| 20. |
- Caceres, L. S., et al.
(author)
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Identification of Excited States in the N = Z Nucleus 82Nb
- 2007
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In: Acta Physica Polonica. Series B: Elementary Particle Physics, Nuclear Physics, Statistical Physics, Theory of Relativity, Field Theory. - 0587-4254. ; 38:4, s. 1271-1275
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Journal article (peer-reviewed)abstract
- Information on the first excited states in the N = Z = 41 nucleus Nb-82 sheds light on the competition of isospin T = 0 and T = 1 states in the A similar to 80 region. The measurement was performed at the GSI laboratory using fragmentation of a Ag-107 primary beam at 750 MeV/u on a 4 g/cm(2) Be-9 target. The fragments were separated and identified unambiguously in the FRagment Separator. Three excited states were observed and the half-life estimate for the isomeric state was extracted. A tentative spin assignment based on the isobaric analogue states systematics in the T-z = 1 nucleus Zr-82, and transition probabilities indicate T = 1 character of the first two excited states, and T = 0 for the isomeric state.
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| 21. |
- Farrelly, G. F., et al.
(author)
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Revision of the K-Isomer in 190W
- 2009
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In: Acta Physica Polonica. Series B: Elementary Particle Physics, Nuclear Physics, Statistical Physics, Theory of Relativity, Field Theory. - 0587-4254. ; 40:3, s. 885-888
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Journal article (peer-reviewed)abstract
- Gamma rays from the decay of an isomer in W-190(116) have been observed following projectile fragmentation of a 1 GeV per nucleon Pb-208 beam. An earlier experiment indicated decay from a (10(-)) isomer to the ground state rotational band. Improved statistics have enabled gamma coincidence and time-difference measurements to be made which alter the previous interpretation. Blocked BCS calculations have also been used together with reduced hindrance factors to indicate possible values of spin-parity for the isomer.
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| 22. |
- Garnsworthy, A. B., et al.
(author)
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Isomeric States in Neutron-deficient A~80-90 Nuclei Populated in the Fragmentation of 107Ag
- 2009
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In: Physical Review C (Nuclear Physics). - 0556-2813. ; 80:6
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Journal article (peer-reviewed)abstract
- The relativistic projectile fragmentation of a 750 MeV per nucleon beam of Ag-107 was used to populate isomeric states in neutron-deficient nuclei around A=80-90. Reaction products were separated and unambiguously identified using the GSI FRagment Separator (FRS) and its ancillary detectors. At the final focal plane, the fragments were slowed from relativistic energies by means of an aluminium degrader and implanted in a passive stopper in the center of the high-efficiency, high-granularity Stopped Rare Isotope Spectroscopic INvestigation at GSI (RISING) germanium array. This allowed the identification of excited states in the N=Z nuclei Tc-86(43) and, for the first time, Nb-82(41). Isomeric states have also been identified for the first time in Tc-87,Tc-88, and a previously unreported isomer was observed in Nb-84. Experimental results are presented along with a discussion on the structure of these nuclei based on interpretations provided by several theoretical models.
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| 23. |
- Garnsworthy, A. B., et al.
(author)
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Isomeric States in the Light Tc Isotopes
- 2007
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In: Acta Physica Polonica. Series B: Elementary Particle Physics, Nuclear Physics, Statistical Physics, Theory of Relativity, Field Theory. - 0587-4254. ; 38:4, s. 1265-1269
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Journal article (peer-reviewed)abstract
- Preliminary results from the first experiment of the Stopped Beam RISING campaign are presented. The relativistic projectile fragmentation of a 750 MeV/u beam of Ag-107 populated isomeric states in very neutron deficient nuclei at the proton dripline around mass 80-90. Nuclei were unambiguously identified using the FRagment Separator (FRS) and its ancillary detectors located at GSI. The ions produced were slowed down from relativistic energies by means of an Al degrader and implanted in the centre of the high-efficiency Stopped RISING array. This allowed the identification of new excited states in the N = Z = 43 nucleus, Tc-86, populated following the de-excitation of a microsecond isomer. Preliminary results of this analysis, as well as previously unobserved isomeric states in Tc-87,Tc-88. are reported.
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| 24. |
- Garnsworthy, A B, et al.
(author)
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Neutron-proton pairing competition in N = Z nuclei: Metastable state decays in the proton dripline nuclei Nb-82(41) and Tc-86(43)
- 2008
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In: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 660:4, s. 326-330
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Journal article (peer-reviewed)abstract
- The low-lying structures of the self-conjugate (N = Z) nuclei Nb-82(41)41 and Tc-86(43)43 have been investigated using isomeric-decay spectroscopy following the projectile fragmentation of a Ag-107 beam. These represent the heaviest odd-odd N = Z nuclei in which internal decays have been identified to date. The resulting level schemes shed light on the shape evolution along the N = Z line between the doubly-magic systems Ni-56(28) and Sn-100(50) and support a preference for T = 1 states in T-z = 0 odd-odd nuclei at low excitation energies associated with a T = 1 neutron-proton pairing gap. Comparison with Projected Shell Model calculations suggests that the decay in Nb-82 may be interpreted as an isospin-changing K isomer.
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| 25. |
- Morales, A. I., et al.
(author)
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beta-delayed gamma-ray spectroscopy of Au-203,Au-204 and Pt200-202
- 2013
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In: Physical Review C (Nuclear Physics). - 0556-2813. ; 88:1
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Journal article (peer-reviewed)abstract
- The beta decay of five heavy, neutron-rich nuclei, Pt-203,Pt-204 and Ir200-202, has been investigated following relativistic cold fragmentation reactions of lead projectiles using the FRS + RISING setup at GSI. This paper reports on the study of the low-lying states in the decay daughter nuclei Au-203,Au-204 and Pt200-202. The characteristic gamma rays for each nucleus have been determined using beta-delayed gamma-ray spectroscopy. Tentative level schemes, relative intensities, and apparent beta feedings are provided. These data are compared with shell-model calculations, which indicate a substantial contribution to the total beta strength from high-energy first-forbidden beta-decay transitions in this mass region.
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