| 1. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 2. |
- Cossarizza, A., et al.
(författare)
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Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)
- 2019
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Ingår i: European Journal of Immunology. - : Wiley. - 0014-2980 .- 1521-4141. ; 49:10, s. 1457-1973
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Tidskriftsartikel (refereegranskat)abstract
- These guidelines are a consensus work of a considerable number of members of the immunology and flow cytometry community. They provide the theory and key practical aspects of flow cytometry enabling immunologists to avoid the common errors that often undermine immunological data. Notably, there are comprehensive sections of all major immune cell types with helpful Tables detailing phenotypes in murine and human cells. The latest flow cytometry techniques and applications are also described, featuring examples of the data that can be generated and, importantly, how the data can be analysed. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid, all written and peer-reviewed by leading experts in the field, making this an essential research companion.
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| 3. |
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| 4. |
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| 5. |
- 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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| 6. |
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| 7. |
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| 8. |
- Mallorquin, M., et al.
(författare)
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TOI-1801 b: A temperate mini-Neptune around a young M0.5 dwarf
- 2023
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Ingår i: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 680
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Tidskriftsartikel (refereegranskat)abstract
- We report the discovery, mass, and radius determination of TOI-1801 b, a temperate mini-Neptune around a young M dwarf. TOI-1801 b was observed in TESS sectors 22 and 49, and the alert that this was a TESS planet candidate with a period of 21.3 days went out in April 2020. However, ground-based follow-up observations, including seeing-limited photometry in and outside transit together with precise radial velocity (RV) measurements with CARMENES and HIRES revealed that the true period of the planet is 10.6 days. These observations also allowed us to retrieve a mass of 5.74 +/- 1.46 M-circle plus, which together with a radius of 2.08 +/- 0.12 R-circle plus, means that TOI-1801 b is most probably composed of water and rock, with an upper limit of 2% by mass of H-2 in its atmosphere. The stellar rotation period of 16 days is readily detectable in our RV time series and in the ground-based photometry. We derived a likely age of 600-800 Myr for the parent star TOI-1801, which means that TOI-1801 b is the least massive young mini-Neptune with precise mass and radius determinations. Our results suggest that if TOI-1801 b had a larger atmosphere in the past, it must have been removed by some evolutionary mechanism on timescales shorter than 1 Gyr.
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| 9. |
- Östling, Jörgen, et al.
(författare)
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IL-17-high asthma with features of a psoriasis immunophenotype
- 2019
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Ingår i: Journal of Allergy and Clinical Immunology. - : Elsevier. - 0091-6749 .- 1097-6825. ; 144:5, s. 1198-1213
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Tidskriftsartikel (refereegranskat)abstract
- Background: The role of IL-17 immunity is well established in patients with inflammatory diseases, such as psoriasis and inflammatory bowel disease, but not in asthmatic patients, in whom further study is required.Objective: We sought to undertake a deep phenotyping study of asthmatic patients with upregulated IL-17 immunity.Methods: Whole-genome transcriptomic analysis was performed by using epithelial brushings, bronchial biopsy specimens (91 asthmatic patients and 46 healthy control subjects), and whole blood samples (n = 498) from the Unbiased Biomarkers for the Prediction of Respiratory Disease Outcomes (U-BIOPRED) cohort. Gene signatures induced in vitro by IL-17 and IL-13 in bronchial epithelial cells were used to identify patients with IL-17–high and IL-13–high asthma phenotypes.Results: Twenty-two of 91 patients were identified with IL-17, and 9 patients were identified with IL-13 gene signatures. The patients with IL-17–high asthma were characterized by risk of frequent exacerbations, airway (sputum and mucosal) neutrophilia, decreased lung microbiota diversity, and urinary biomarker evidence of activation of the thromboxane B2 pathway. In pathway analysis the differentially expressed genes in patients with IL-17-high asthma were shared with those reported as altered in psoriasis lesions and included genes regulating epithelial barrier function and defense mechanisms, such as IL1B, IL6, IL8, and β-defensin.Conclusion: The IL-17–high asthma phenotype, characterized by bronchial epithelial dysfunction and upregulated antimicrobial and inflammatory response, resembles the immunophenotype of psoriasis, including activation of the thromboxane B2 pathway, which should be considered a biomarker for this phenotype in further studies, including clinical trials targeting IL-17.
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| 10. |
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| 11. |
- Brinkman, D. M., et al.
(författare)
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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
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Ingår i: Arthritis Rheum. - : Wiley. - 0004-3591. ; 56:7, s. 2410-21
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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.
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| 12. |
- Clark, R M, et al.
(författare)
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Superdeformation in bismuth
- 1996
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Ingår i: Physical Review C. Nuclear Physics. - 0556-2813 .- 1089-490X. ; 53:1, s. 117-123
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Tidskriftsartikel (refereegranskat)abstract
- High angular momentum states in Bi-195-197 are populated in two reactions: W-183(F-19,xn)Bi-202-x and Ta-181(Ne-20,xn)Bi-201-x at beam energies of 108 and 123 MeV, respectively. Gamma rays were detected using the Gammasphere array. Three weakly populated rotational sequences have been found. They each have properties characteristic of other superdeformed bands in this mass region. On the basis of cross-bombardment information we believe that one band belongs to each of Bi-195, Bi-196, and Bi-197. The properties of the bands in the odd-Bi nuclei are best reproduced if the odd proton occupies the favored signature of the [651]1/2 orbital, while the band in Bi-196 has this same proton configuration coupled to an additional N=7 (j(15/2)) neutron. The relative behavior of the J((2)) moments of inertia can be qualitatively understood in terms of Pauli-blocking effects.
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| 13. |
- de Kleer, I. M., et al.
(författare)
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Autologous stem cell transplantation for refractory juvenile idiopathic arthritis: analysis of clinical effects, mortality, and transplant related morbidity
- 2004
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Ingår i: Ann Rheum Dis. - : BMJ. - 0003-4967. ; 63:10, s. 1318-26
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: To evaluate the safety and efficacy of autologous stem cell transplantation (ASCT) for refractory juvenile idiopathic arthritis (JIA). DESIGN: Retrospective analysis of follow up data on 34 children with JIA who were treated with ASCT in nine different European transplant centres. Rheumatological evaluation employed a modified set of core criteria. Immunological reconstitution and infectious complications were monitored at three month intervals after transplantation. RESULTS: Clinical follow up ranged from 12 to 60 months. Eighteen of the 34 patients (53%) with a follow up of 12 to 60 months achieved complete drug-free remission. Seven of these patients had previously failed treatment with anti-TNF. Six of the 34 patients (18%) showed a partial response (ranging from 30% to 70% improvement) and seven (21%) were resistant to ASCT. Infectious complications were common. There were three cases of transplant related mortality (9%) and two of disease related mortality (6%). CONCLUSIONS: ASCT in severely ill patients with JIA induces a drug-free remission of the disease and a profound increase in general wellbeing in a substantial proportion of patients, but the procedure carries a significant mortality risk. The following adjustments are proposed for future protocols: (1) elimination of total body irradiation from the conditioning regimen; (2) prophylactic administration of antiviral drugs and intravenous immunoglobulins until there is a normal CD4+ T cell count.
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| 14. |
- Baldsiefen, G, et al.
(författare)
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Shears bands in Pb-193
- 1996
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Ingår i: Physical Review C. Nuclear Physics. - 0556-2813 .- 1089-490X. ; 54:3, s. 1106-1116
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Tidskriftsartikel (refereegranskat)abstract
- Four bands of enhanced dipole transitions, with weak crossovers, have been observed in Pb-195. Three of these bands are connected to the spherical levels. in addition, the spherical level scheme has been extended. The nuclear spectroscopy was done with the early implementation of GAMMASPHERE and HERA arrays of Get detectors. The nucleus Pb-193 was populated in the Yb-174(Mg-24,5n) reaction at beam energies of 129, 131, and 134 MeV. The experimental results are compared to tilted-axis cranking calculations. The systematical behavior of the dipole bands in the heavier odd-A Pb isotopes, Pb-195,Pb-197,Pb-199,Pb-201, is also discussed.
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| 15. |
- Djoussé, L, et al.
(författare)
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Interaction of normal and expanded CAG repeat sizes influences age at onset of Huntington disease.
- 2003
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Ingår i: American Journal of Medical Genetics. Part A. - : Wiley. - 1552-4825 .- 1552-4833. ; 119A:3, s. 279-82
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Tidskriftsartikel (refereegranskat)abstract
- Huntington disease (HD) is a neurodegenerative disorder caused by the abnormal expansion of CAG repeats in the HD gene on chromosome 4p16.3. Past studies have shown that the size of expanded CAG repeat is inversely associated with age at onset (AO) of HD. It is not known whether the normal Huntington allele size influences the relation between the expanded repeat and AO of HD. Data collected from two independent cohorts were used to test the hypothesis that the unexpanded CAG repeat interacts with the expanded CAG repeat to influence AO of HD. In the New England Huntington Disease Center Without Walls (NEHD) cohort of 221 HD affected persons and in the HD-MAPS cohort of 533 HD affected persons, we found evidence supporting an interaction between the expanded and unexpanded CAG repeat sizes which influences AO of HD (P = 0.08 and 0.07, respectively). The association was statistically significant when both cohorts were combined (P = 0.012). The estimated heritability of the AO residual was 0.56 after adjustment for normal and expanded repeats and their interaction. An analysis of tertiles of repeats sizes revealed that the effect of the normal allele is seen among persons with large HD repeat sizes (47-83). These findings suggest that an increase in the size of the normal repeat may mitigate the expression of the disease among HD affected persons with large expanded CAG repeats.
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| 16. |
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| 17. |
- Horvath, I., et al.
(författare)
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A European Respiratory Society technical standard: exhaled biomarkers in lung disease
- 2017
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Ingår i: European Respiratory Journal. - : European Respiratory Society (ERS). - 0903-1936 .- 1399-3003. ; 49:4
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Tidskriftsartikel (refereegranskat)abstract
- Breath tests cover the fraction of nitric oxide in expired gas (FeNO), volatile organic compounds (VOCs), variables in exhaled breath condensate (EBC) and other measurements. For EBC and for FeNO, official recommendations for standardised procedures are more than 10 years old and there is none for exhaled VOCs and particles. The aim of this document is to provide technical standards and recommendations for sample collection and analytic approaches and to highlight future research priorities in the field. For EBC and FeNO, new developments and advances in technology have been evaluated in the current document. This report is not intended to provide clinical guidance on disease diagnosis and management. Clinicians and researchers with expertise in exhaled biomarkers were invited to participate. Published studies regarding methodology of breath tests were selected, discussed and evaluated in a consensus-based manner by the Task Force members. Recommendations for standardisation of sampling, analysing and reporting of data and suggestions for research to cover gaps in the evidence have been created and summarised. Application of breath biomarker measurement in a standardised manner will provide comparable results, thereby facilitating the potential use of these biomarkers in clinical practice.
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| 18. |
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| 19. |
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| 20. |
- Smid, Marcel, et al.
(författare)
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Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration
- 2016
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- A recent comprehensive whole genome analysis of a large breast cancer cohort was used to link known and novel drivers and substitution signatures to the transcriptome of 266 cases. Here, we validate that subtype-specific aberrations show concordant expression changes for, for example, TP53, PIK3CA, PTEN, CCND1 and CDH1. We find that CCND3 expression levels do not correlate with amplification, while increased GATA3 expression in mutant GATA3 cancers suggests GATA3 is an oncogene. In luminal cases the total number of substitutions, irrespective of type, associates with cell cycle gene expression and adverse outcome, whereas the number of mutations of signatures 3 and 13 associates with immune-response specific gene expression, increased numbers of tumour-infiltrating lymphocytes and better outcome. Thus, while earlier reports imply that the sheer number of somatic aberrations could trigger an immune-response, our data suggests that substitutions of a particular type are more effective in doing so than others.
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| 21. |
- Turtelboom,, et al.
(författare)
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The TESS-Keck Survey. XI. Mass Measurements for Four Transiting Sub-Neptunes Orbiting K Dwarf TOI-1246
- 2022
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Ingår i: Astronomical Journal. - : American Astronomical Society. - 1538-3881 .- 0004-6256. ; 163:6
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Tidskriftsartikel (refereegranskat)abstract
- Multiplanet systems are valuable arenas for investigating exoplanet architectures and comparing planetary siblings. TOI-1246 is one such system, with a moderately bright K dwarf (V = 11.6, K = 9.9) and four transiting sub-Neptunes identified by TESS with orbital periods of 4.31, 5.90, 18.66, and 37.92 days. We collected 130 radial velocity observations with Keck/HIRES and TNG/HARPS-N to measure planet masses. We refit the 14 sectors of TESS photometry to refine planet radii (2.97 +/- 0.06 R (circle plus), 2.47 +/- 0.08 R (circle plus), 3.46 +/- 0.09 R (circle plus), and 3.72 +/- 0.16 R (circle plus)) and confirm the four planets. We find that TOI-1246 e is substantially more massive than the three inner planets (8.1 +/- 1.1 M (circle plus), 8.8 +/- 1.2 M (circle plus), 5.3 +/- 1.7 M (circle plus), and 14.8 +/- 2.3 M (circle plus)). The two outer planets, TOI-1246 d and TOI-1246 e, lie near to the 2:1 resonance (P (e)/P ( d ) = 2.03) and exhibit transit-timing variations. TOI-1246 is one of the brightest four-planet systems, making it amenable for continued observations. It is one of only five systems with measured masses and radii for all four transiting planets. The planet densities range from 0.70 +/- 0.24 to 3.21 +/- 0.44 g cm(-3), implying a range of bulk and atmospheric compositions. We also report a fifth planet candidate found in the RV data with a minimum mass of 25.6 +/- 3.6 M (circle plus). This planet candidate is exterior to TOI-1246 e, with a candidate period of 93.8 days, and we discuss the implications if it is confirmed to be planetary in nature.
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| 22. |
- Brinkman, M J, et al.
(författare)
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Decay from a superdeformed band in Pb-194
- 1996
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Ingår i: Physical Review C. Nuclear Physics. - 0556-2813 .- 1089-490X. ; 53:4, s. R1461-R1464
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Tidskriftsartikel (refereegranskat)abstract
- Three experiments using the (174) Yb(Mg-25,5n)Pb-194 reaction have been undertaken at the Early Implementation of Gammasphere to study the decay of known superdeformed states in Pb-194. A single discrete transition with an energy of 2.746(2) MeV carrying 6(2)% of the full superdeformed band intensity has been identified. A discussion of our results and the assignment of the 2.746-MeV transition as a discrete gamma ray directly connecting the superdeformed 8(+) and low-lying 6(+) levels will be presented.
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| 23. |
- Bruce, A. M., et al.
(författare)
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Two-neutron alignment and shape changes in As-69
- 2000
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Ingår i: Physical Review C. Nuclear Physics. - 0556-2813 .- 1089-490X. ; 6202:2
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Tidskriftsartikel (refereegranskat)abstract
- The nucleus As-69 was Studied using the Ca-40(S-32,3p)As-69 reaction at a beam energy of 105 MeV. An extension of the band built on the g(9/2) orbital was observed to exhibit a band crossing at a rotational frequency of 0.511 MeV with an associated alignment of 7 (h) over bar. This alignment is interpreted as being due to a pair of g(9/2) neutrons. Total Routhian surface calculations have been carried out which confirm that the shape of this nucleus changes from oblate at low spin to a triaxial prolate shape at intermediate spin.
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| 24. |
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| 25. |
- Papini, Chiara, et al.
(författare)
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Evolving therapies, neurocognitive outcomes, and functional independence in adult survivors of childhood glioma
- 2024
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Ingår i: Journal of the National Cancer Institute. - 0027-8874. ; 116:2, s. 288-298
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Tidskriftsartikel (refereegranskat)abstract
- Background: Treatment of childhood glioma has evolved to reduce radiotherapy exposure with the goal of limiting late toxicity. However, the associations between treatment changes and neurocognition, and the contribution of neurocognition and chronic health conditions to attainment of adult independence, remain unknown. Methods: Adult survivors of childhood glioma diagnosed in 1970-1999 in the Childhood Cancer Survivor Study (n ¼ 1284; median [minimum-maximum] 30 [18-51] years of age at assessment; 22 [15-34] years from diagnosis) self-reported neurocognitive impairment and chronic health conditions. Multivariable models evaluated associations between changes in treatment exposures (surgery only, chemotherapy [with or without surgery], cranial radiation [with or without chemotherapy and/or surgery]), and neurocognitive impairment. Latent class analysis with 5 indicators (employment, independent living, assistance with routine and/or personal care needs, driver’s license, marital or partner status) identified classes of functional independence. Path analysis tested associations among treatment exposures, neurocognitive impairment, chronic health conditions, and functional independence. Statistical tests were 2-sided. Results: Cranial radiation exposure decreased over time (51%, 1970s; 46%, 1980s; 27%, 1990s]. However, compared with siblings, survivors with any treatment exposure were at elevated risk for neurocognitive impairment, including surgery only (eg, memory: relative risk ¼ 2.22; task efficiency: relative risk ¼ 1.88; both P < .001). Three classes of functional independence were identified: independent (58%), moderately independent (20%), and nonindependent (22%). Cranial radiation was associated with nonindependence through impaired task efficiency (b ¼ 0.06), sensorimotor (b ¼ 0.06), and endocrine (b ¼ 0.10) chronic health conditions and through the associations between these conditions and task efficiency (each b ¼ 0.04). Sensorimotor and endocrine chronic health conditions were associated with nonindependence through memory. Conclusion: Most long-term glioma survivors achieve adult independence. However, functional nonindependence is associated with treatment-related neurocognitive impairment and chronic health conditions.
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| 26. |
- Rosenblatt, A, et al.
(författare)
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Familial influence on age of onset among siblings with Huntington disease.
- 2001
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Ingår i: American Journal of Medical Genetics. - 0148-7299 .- 1096-8628. ; 105:5, s. 399-403
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Tidskriftsartikel (refereegranskat)abstract
- In order to provide data relevant to a search for modifying genes for age of onset in Huntington disease, we examined the relationship between CAG number and age of onset in a total of 370 individuals from 165 siblingships, in two cohorts of siblings with Huntington disease: an American group of 144 individuals from 64 siblingships, and a Canadian population of 255 individuals from 113 siblingships. Using a logarithmic model to regress the age of onset on the number of CAG triplets, we found that CAG number alone accounted for 65%-71% of the variance in age of onset. The siblingship an individual belonged to accounted for 11%-19% of additional variance. This adds to the previous evidence that there are familial modifiers of the age of onset, independent of the CAG number. Such modifiers may consist of additional genes, which could be the target of a linkage study. A linkage study is feasible with the cooperation of a number of major centers and may be made more efficient by concentrating on sibling pairs that are highly discordant for age of onset.
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| 27. |
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| 28. |
- Abdel-Aziz, MI, et al.
(författare)
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A System Pharmacology Multi-Omics Approach toward Uncontrolled Pediatric Asthma
- 2021
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Ingår i: Journal of personalized medicine. - : MDPI AG. - 2075-4426. ; 11:6
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Tidskriftsartikel (refereegranskat)abstract
- There is a clinical need to identify children with poor asthma control as early as possible, to optimize treatment and/or to find therapeutic alternatives. Here, we present the “Systems Pharmacology Approach to Uncontrolled Pediatric Asthma” (SysPharmPediA) study, which aims to establish a pediatric cohort of moderate-to-severe uncontrolled and controlled patients with asthma, to investigate pathophysiological mechanisms underlying uncontrolled moderate-to-severe asthma in children on maintenance treatment, using a multi-omics systems medicine approach. In this multicenter observational case–control study, moderate-to-severe asthmatic children (age; 6–17 years) were included from four European countries (Netherlands, Germany, Spain, and Slovenia). Subjects were classified based on asthma control and number of exacerbations. Demographics, current and past patient/family history, and clinical characteristics were collected. In addition, systems-wide omics layers, including epi(genomics), transcriptomics, microbiome, proteomics, and metabolomics were evaluated from multiple samples. In all, 145 children were included in this cohort, 91 with uncontrolled (median age = 12 years, 43% females) and 54 with controlled asthma (median age = 11.7 years, 37% females). The two groups did not show statistically significant differences in age, sex, and body mass index z-score distribution. Comprehensive information and diverse noninvasive biosampling procedures for various omics analyses will provide the opportunity to delineate underlying pathophysiological mechanisms of moderate-to-severe uncontrolled pediatric asthma. This eventually might reveal novel biomarkers, which could potentially be used for noninvasive personalized diagnostics and/or treatment.
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| 29. |
- Beard, Corey, et al.
(författare)
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The TESS-Keck Survey. XVII. Precise Mass Measurements in a Young, High-multiplicity Transiting Planet System Using Radial Velocities and Transit Timing Variations
- 2024
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Ingår i: Astronomical Journal. - 1538-3881 .- 0004-6256. ; 167:2
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Tidskriftsartikel (refereegranskat)abstract
- We present a radial velocity (RV) analysis of TOI-1136, a bright Transiting Exoplanet Survey Satellite (TESS) system with six confirmed transiting planets, and a seventh single-transiting planet candidate. All planets in the system are amenable to transmission spectroscopy, making TOI-1136 one of the best targets for intra-system comparison of exoplanet atmospheres. TOI-1136 is young (similar to 700 Myr), and the system exhibits transit timing variations (TTVs). The youth of the system contributes to high stellar variability on the order of 50 m s-1, much larger than the likely RV amplitude of any of the transiting exoplanets. Utilizing 359 High Resolution Echelle Spectrometer and Automated Planet Finder RVs collected as part of the TESS-Keck Survey, and 51 High-Accuracy Radial velocity Planetary Searcher North RVs, we experiment with a joint TTV-RV fit. With seven possible transiting planets, TTVs, more than 400 RVs, and a stellar activity model, we posit that we may be presenting the most complex mass recovery of an exoplanet system in the literature to date. By combining TTVs and RVs, we minimized Gaussian process overfitting and retrieved new masses for this system: (m b-g = 3.50-0.7+0.8 , 6.32-1.3+1.1 , 8.35-1.6+1.8 , 6.07-1.01+1.09 , 9.7-3.7+3.9 , 5.6-3.2+4.1 M circle plus). We are unable to significantly detect the mass of the seventh planet candidate in the RVs, but we are able to loosely constrain a possible orbital period near 80 days. Future TESS observations might confirm the existence of a seventh planet in the system, better constrain the masses and orbital properties of the known exoplanets, and generally shine light on this scientifically interesting system.
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| 30. |
- Brinkman, D. J., et al.
(författare)
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Essential Competencies in Prescribing: A First European Cross-Sectional Study Among 895 Final-Year Medical Students
- 2017
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Ingår i: Clinical Pharmacology and Therapeutics. - : WILEY-BLACKWELL. - 0009-9236 .- 1532-6535. ; 101:2, s. 281-289
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Tidskriftsartikel (refereegranskat)abstract
- European medical students should have acquired adequate prescribing competencies before graduation, but it is not known whether this is the case. In this international multicenter study, we evaluated the essential knowledge, skills, and attitudes in clinical pharmacology and therapeutics (CPT) of final-year medical students across Europe. In a cross-sectional design, 26 medical schools from 17 European countries were asked to administer a standardized assessment and questionnaire to 50 final-year students. Although there were differences between schools, our results show an overall lack of essential prescribing competencies among final-year students in Europe. Students had a poor knowledge of drug interactions and contraindications, and chose inappropriate therapies for common diseases or made prescribing errors. Our results suggest that undergraduate teaching in CPT is inadequate in many European schools, leading to incompetent prescribers and potentially unsafe patient care. A European core curriculum with clear learning outcomes and assessments should be urgently developed.
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| 31. |
- Brinkman, R R, et al.
(författare)
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The likelihood of being affected with Huntington disease by a particular age, for a specific CAG size.
- 1997
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Ingår i: American Journal of Human Genetics. - 0002-9297 .- 1537-6605. ; 60:5, s. 1202-10
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Tidskriftsartikel (refereegranskat)abstract
- Prior studies describing the relationship between CAG size and the age at onset of Huntington disease (HD) have focused on affected persons. To further define the relationship between CAG repeat size and age at onset of HD, we now have analyzed a large cohort of affected and asymptomatic at-risk persons with CAG expansion. This cohort numbered 1,049 persons, including 321 at-risk and 728 affected individuals with a CAG size of 29-121 repeats. Kaplan-Meier analysis has provided curves for determining the likelihood of onset at a given age, for each CAG repeat length in the 39-50 range. The curves were significantly different (P < .0005), with relatively narrow 95% confidence intervals (95% CI) (+/-10%). Penetrance of the mutation for HD also was examined. Although complete penetrance of HD was observed for CAG sizes of > or = 42, only a proportion of those with a CAG repeat length of 36-41 showed signs or symptoms of HD within a normal life span. These data provide information concerning the likelihood of being affected, by a specific age, with a particular CAG size, and they may be useful in predictive-testing programs and for the design of clinical trials for persons at increased risk for HD.
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| 32. |
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| 33. |
- LaFosse, D R, et al.
(författare)
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Search for hyperdeformation in Gd-146,Gd-147
- 1996
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Ingår i: Physical Review C. Nuclear Physics. - 0556-2813 .- 1089-490X. ; 54:4, s. 1585-1588
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Tidskriftsartikel (refereegranskat)abstract
- A search was undertaken to look for evidence of hyperdeformation in Gd-146,Gd-147. Three experiments employing Gammasphere for gamma-ray detection coupled with the Microball for channel selection via charged particle detection were carried out with increasing detection sensitivity and statistics. No definitive evidence for band structures that could be assigned to hyperdeformation could be found. Candidates previously reported are shown not to have properties consistent with a band structure.
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| 34. |
- Morganella, Sandro, et al.
(författare)
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The topography of mutational processes in breast cancer genomes
- 2016
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Somatic mutations in human cancers show unevenness in genomic distribution that correlate with aspects of genome structure and function. These mutations are, however, generated by multiple mutational processes operating through the cellular lineage between the fertilized egg and the cancer cell, each composed of specific DNA damage and repair components and leaving its own characteristic mutational signature on the genome. Using somatic mutation catalogues from 560 breast cancer whole-genome sequences, here we show that each of 12 base substitution, 2 insertion/deletion (indel) and 6 rearrangement mutational signatures present in breast tissue, exhibit distinct relationships with genomic features relating to transcription, DNA replication and chromatin organization. This signature-based approach permits visualization of the genomic distribution of mutational processes associated with APOBEC enzymes, mismatch repair deficiency and homologous recombinational repair deficiency, as well as mutational processes of unknown aetiology. Furthermore, it highlights mechanistic insights including a putative replication-dependent mechanism of APOBEC-related mutagenesis.
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| 35. |
- Nik-Zainal, Serena, et al.
(författare)
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Landscape of somatic mutations in 560 breast cancer whole-genome sequences
- 2016
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 534:7605, s. 47-54
-
Tidskriftsartikel (refereegranskat)abstract
- We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.
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| 36. |
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| 37. |
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| 38. |
- Abdel-Aziz, Mahmoud I., et al.
(författare)
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A multi-omics approach to delineate sputum microbiome-associated asthma inflammatory phenotypes
- 2022
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Ingår i: European Respiratory Journal. - : European Respiratory Society. - 0903-1936 .- 1399-3003. ; 59:1
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Tidskriftsartikel (refereegranskat)abstract
- A multi-omics approach revealed the underlying biological pathways in the microbiome-driven severe asthma phenotypes. This may help to elucidate new leads for treatment development, particularly for the therapeutically challenging neutrophilic asthma.
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| 39. |
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| 40. |
- Almqvist, E W, et al.
(författare)
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A worldwide assessment of the frequency of suicide, suicide attempts, or psychiatric hospitalization after predictive testing for Huntington disease.
- 1999
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Ingår i: American Journal of Human Genetics. - 0002-9297 .- 1537-6605. ; 64:5, s. 1293-304
-
Tidskriftsartikel (refereegranskat)abstract
- Prior to the implementation of predictive-testing programs for Huntington disease (HD), significant concern was raised concerning the likelihood of catastrophic events (CEs), particularly in those persons receiving an increased-risk result. We have investigated the frequency of CEs-that is, suicide, suicide attempt, and psychiatric hospitalization-after an HD predictive-testing result, through questionnaires sent to predictive-testing centers worldwide. A total of 44 persons (0.97%) in a cohort of 4,527 test participants had a CE: 5 successful suicides, 21 suicide attempts, and 18 hospitalizations for psychiatric reasons. All persons committing suicide had signs of HD, whereas 11 (52.4%) of 21 persons attempting suicide and 8 (44.4%) of 18 who had a psychiatric hospitalization were symptomatic. A total of 11 (84.6%) of 13 asymptomatic persons who experienced a CE during the first year after HD predictive testing received an increased-risk result. Factors associated with an increased risk of a CE included (a) a psychiatric history
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| 41. |
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| 42. |
- Glodzik, Dominik, et al.
(författare)
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A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers
- 2017
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 49:3, s. 341-348
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Tidskriftsartikel (refereegranskat)abstract
- Somatic rearrangements contribute to the mutagenized landscape of cancer genomes. Here, we systematically interrogated rearrangements in 560 breast cancers by using a piecewise constant fitting approach. We identified 33 hotspots of large (>100 kb) tandem duplications, a mutational signature associated with homologous-recombination-repair deficiency. Notably, these tandem-duplication hotspots were enriched in breast cancer germline susceptibility loci (odds ratio (OR) = 4.28) and breast-specific 'super-enhancer' regulatory elements (OR = 3.54). These hotspots may be sites of selective susceptibility to double-strand-break damage due to high transcriptional activity or, through incrementally increasing copy number, may be sites of secondary selective pressure. The transcriptomic consequences ranged from strong individual oncogene effects to weak but quantifiable multigene expression effects. We thus present a somatic-rearrangement mutational process affecting coding sequences and noncoding regulatory elements and contributing a continuum of driver consequences, from modest to strong effects, thereby supporting a polygenic model of cancer development.
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| 43. |
- Hon, Marc, et al.
(författare)
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A close-in giant planet escapes engulfment by its star
- 2023
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Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 618:7967, s. 917-920
-
Tidskriftsartikel (refereegranskat)abstract
- When main-sequence stars expand into red giants, they are expected to engulf close-in planets(1-5). Until now, the absence of planets with short orbital periods around post-expansion, core-helium-burning red giants(6-8) has been interpreted as evidence that short-period planets around Sun-like stars do not survive the giant expansion phase of their host stars(9). Here we present the discovery that the giant planet 8 Ursae Minoris b(10) orbits a core-helium-burning red giant. At a distance of only 0.5 au from its host star, the planet would have been engulfed by its host star, which is predicted by standard single-star evolution to have previously expanded to a radius of 0.7 au. Given the brief lifetime of helium-burning giants, the nearly circular orbit of the planet is challenging to reconcile with scenarios in which the planet survives by having a distant orbit initially. Instead, the planet may have avoided engulfment through a stellar merger that either altered the evolution of the host star or produced 8 Ursae Minoris b as a second-generation planet(11). This system shows that core-helium-burning red giants can harbour close planets and provides evidence for the role of non-canonical stellar evolution in the extended survival of late-stage exoplanetary systems.
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| 44. |
- LAFOSSE, DR, et al.
(författare)
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CHARACTERIZATION OF THE FIRST SUPERDEFORMED BAND IN THE A-APPROXIMATE-TO-80 REGION
- 1995
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Ingår i: Physics Letters B. - 0370-2693 .- 1873-2445. ; 354:1-2, s. 34-40
-
Tidskriftsartikel (refereegranskat)abstract
- The recently discovered superdeformed band in one of the strontium isotopes has been identified as belonging to Sr-83 from a study with the Gammasphere array and the Microball charged-particle detector system. From its decay pattern, a spin of (81 +/- 2)/2 ($) over bar h is deduced for the highest level of this band. Evidence for very fast transition rates and agreement of the characteristics of this band with the theoretical predictions establish the yrast superdeformed nature of this band in Sr-83.
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| 45. |
- Rudolph, Dirk, et al.
(författare)
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High-spin Shell-model States Near 56Ni
- 1999
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Ingår i: European Physical Journal A. Hadrons and Nuclei. - 1434-6001. ; 4:2, s. 115-145
-
Tidskriftsartikel (refereegranskat)abstract
- High-spin states of nuclei near doubly magic Ni-56 were studied with the reaction Si-28(Ar-36, xpynz alpha) at 136 MeV beam energy. The GAMMASPHERE array in conjunction with the 4 pi charged-particle detector array MICROBALL and neutron detectors were used to detect gamma rays in coincidence with evaporated light particles. The resulting extensive decay schemes of Fe-54, Co-54,Co-55, Ni-56,Ni-57, and Cu-58 are compared to shell model calculations in the fp shell.
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| 46. |
- Rudolph, Dirk, et al.
(författare)
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Rotational Bands in the Doubly Magic Nucleus 56Ni
- 1999
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Ingår i: Physical Review Letters. - 1079-7114. ; 82:19, s. 3763-3766
-
Tidskriftsartikel (refereegranskat)abstract
- Structures of the medium- to high-spin states in the doubly magic nucleus Ni-56 have been investigated using the reaction Si-28(Ar-36, 2 alpha) and the gamma-ray spectrometer Gammasphere in conjunction with the 4 pi charged-particle detector array Microball. Two well-deformed rotational bands have been identified. There is evidence that one of the bands, which is identical to a sequence in the odd-odd neighbor Cu-58, partially decays via proton emission into the ground state of Co-55. Predictions of extensive large-scale shell-model and cranked Hartree-Fock and Hartree-Fock-Bogolyubov calculations are compared with the experimental data.
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| 47. |
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| 48. |
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| 49. |
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| 50. |
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