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| 2. |
- Gyllenberg, A, et al.
(författare)
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Age-dependent variation of genotypes in MHC II transactivator gene (CIITA) in controls and association to type 1 diabetes
- 2012
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Ingår i: Genes and Immunity. - Stockholm : Springer Science and Business Media LLC. - 1476-5470 .- 1466-4879. ; 76:2, s. 202-203
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Tidskriftsartikel (refereegranskat)abstract
- The major histocompatibility complex class II transactivator (CIITA) gene (16p13) has been reported to associate with susceptibility to multiple sclerosis, rheumatoid arthritis and myocardial infarction, recently also to celiac disease at genome-wide level. However, attempts to replicate association have been inconclusive. Previously, we have observed linkage to the CIITA region in Scandinavian type 1 diabetes (T1D) families. Here we analyze five Swedish T1D cohorts and a combined control material from previous studies of CIITA. We investigate how the genotype distribution within the CIITA gene varies depending on age, and the association to T1D. Unexpectedly, we find a significant difference in the genotype distribution for markers in CIITA (rs11074932, P=4 × 10(-5) and rs3087456, P=0.05) with respect to age, in the collected control material. This observation is replicated in an independent cohort material of about 2000 individuals (P=0.006, P=0.007). We also detect association to T1D for both markers, rs11074932 (P=0.004) and rs3087456 (P=0.001), after adjusting for age at sampling. The association remains independent of the adjacent T1D risk gene CLEC16A. Our results indicate an age-dependent variation in CIITA allele frequencies, a finding of relevance for the contrasting outcomes of previously published association studies.
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| 3. |
- Jones, Felicity C., et al.
(författare)
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The genomic basis of adaptive evolution in threespine sticklebacks
- 2012
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 484:7392, s. 55-61
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Tidskriftsartikel (refereegranskat)abstract
- Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.
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| 4. |
- King, P.D.C., et al.
(författare)
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Large Tunable Rashba Spin Splitting of a Two-Dimensional Electron Gas in Bi2Se3
- 2011
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Ingår i: Physical Review Letters. - : aps physics. ; 107:9
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Tidskriftsartikel (refereegranskat)abstract
- We report a Rashba spin splitting of a two-dimensional electron gas in the topological insulator Bi2Se3 from angle-resolved photoemission spectroscopy. We further demonstrate its electrostatic control, and show that spin splittings can be achieved which are at least an order-of-magnitude larger than in other semiconductors. Together these results show promise for the miniaturization of spintronic devices to the nanoscale and their operation at room temperature.
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| 5. |
- Lindblad-Toh, Kerstin, et al.
(författare)
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A high-resolution map of human evolutionary constraint using 29 mammals
- 2011
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 478:7370, s. 476-482
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Tidskriftsartikel (refereegranskat)abstract
- The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering similar to 4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for similar to 60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate-and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.
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| 6. |
- Andersson, C, et al.
(författare)
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Triple specificity of ZnT8 autoantibodies in relation to HLA and other islet autoantibodies in childhood and adolescent type 1 diabetes
- 2013
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Ingår i: Pediatric Diabetes. - : Wiley-Blackwell. - 1399-543X .- 1399-5448. ; 14:2, s. 97-105
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Tidskriftsartikel (refereegranskat)abstract
- Andersson C, Vaziri-Sani F, Delli AJ, Lindblad B, Carlsson A, Forsander G, Ludvigsson J, Marcus C, Samuelsson U, Ivarsson SA, Lernmark A, Elding Larsson H, the BDD Study group. Triple specificity of ZnT8 autoantibodies in relation to HLA and other islet autoantibodies in childhood and adolescent type 1 diabetes. Pediatric Diabetes 2013: 14: 97-105. Objective To establish the diagnostic sensitivity of and the relationships between autoantibodies to all three Zinc transporter 8 (Zinc transporter 8 autoantibody to either one, two, or all three amino acid variants at position 325, ZnT8A) variants to human leukocyte antigen (HLA)-DQ and to autoantibodies to glutamic acid decarboxylase (GADA), insulinoma-associated protein 2 (IA-2A), and insulin (IAA). Methods We analyzed 3165 patients with type 1 diabetes (T1D) in the Better Diabetes Diagnosis study for HLA-DQ genotypes and all six autoantibodies (ZnT8RA, arginine 325 Zinc transporter 8 autoantibody; ZnT8WA, tryptophan 325 Zinc transporter 8 autoantibody; ZnT8QA, glutamine 325 Zinc transporter 8 autoantibody; GADA, IA-2A, and IAA). Results ZnT8A was found in 65% of the patients and as many as 108 of 3165 (3.4%) had 13 ZnT8A alone. None had ZnT8QA alone. Together with GADA (56%), IA-2A (73%), and IAA (33%), 93% of the T1D patients were autoantibody positive. All three ZnT8A were less frequent in children below 2 yr of age (pandlt;0.0001). All three ZnT8A were associated with DQA1-B1*X-0604 (DQ6.4) and DQA1-B1*03-0302 (DQ8). ZnT8WA and ZnT8QA were negatively associated with DQA1-B1*05-02 (DQ2). Conclusions Analysis of ZnT8A increased the diagnostic sensitivity of islet autoantibodies for T1D as only 7% remained islet autoantibody negative. The association between DQ6.4 and all three ZnT8A may be related to ZnT8 antigen presentation by the DQ6.4 heterodimer.
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| 7. |
- Frantz, A M, et al.
(författare)
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Molecular Profiling Reveals Prognostically Significant Subtypes of Canine Lymphoma
- 2013
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Ingår i: Veterinary pathology. - : SAGE Publications. - 0300-9858 .- 1544-2217. ; 50:4, s. 693-703
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Tidskriftsartikel (refereegranskat)abstract
- We performed genomewide gene expression analysis of 35 samples representing 6 common histologic subtypes of canine lymphoma and bioinformatics analyses to define their molecular characteristics. Three major groups were defined on the basis of gene expression profiles: (1) low-grade T-cell lymphoma, composed entirely by T-zone lymphoma; (2) high-grade T-cell lymphoma, consisting of lymphoblastic T-cell lymphoma and peripheral T-cell lymphoma not otherwise specified; and (3) B-cell lymphoma, consisting of marginal B-cell lymphoma, diffuse large B-cell lymphoma, and Burkitt lymphoma. Interspecies comparative analyses of gene expression profiles also showed that marginal B-cell lymphoma and diffuse large B-cell lymphoma in dogs and humans might represent a continuum of disease with similar drivers. The classification of these diverse tumors into 3 subgroups was prognostically significant, as the groups were directly correlated with event-free survival. Finally, we developed a benchtop diagnostic test based on expression of 4 genes that can robustly classify canine lymphomas into one of these 3 subgroups, enabling a direct clinical application for our results.
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| 8. |
- Kimberg, V., et al.
(författare)
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Single-Molecule X-Ray Interferometry : Controlling Coupled Electron-Nuclear Quantum Dynamics and Imaging Molecular Potentials by Ultrahigh-Resolution Resonant Photoemission and Ab Initio Calculations
- 2013
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Ingår i: Physical Review X. - : American Physical Society. - 2160-3308. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- This paper reports an advanced study of the excited ionic states of the gas-phase nitrogen molecule in the binding-energy region of 22-34 eV, combining ultrahigh-resolution resonant photoemission (RPE) and ab initio configuration-interaction calculations. The RPE spectra are recorded for nine photon energies within the N 1s -> pi* absorption resonance of N-2 by using a photon bandwidth that is considerably smaller than lifetime broadening, and the dependence on excitation energy of the decay spectra is analyzed and used for the first assignment of 12 highly overlapped molecular states. The effect on the RPE profile of avoided curve crossings between the final N-2(+) ionic states is discussed, based on theoretical simulations that account for vibronic coupling, and compared with the experimental data. By use of synchrotron radiation with high spectral brightness, it is possible to selectively promote the molecule to highly excited vibrational sublevels of a core-excited electronic state, thereby controlling the spatial distribution of the vibrational wave packets, and to accurately image the ionic molecular potentials. In addition, the mapping of the vibrational wave functions of the core-excited states using the bound final states with far-from-equilibrium bond lengths has been achieved experimentally for the first time. Theoretical analysis has revealed the rich femtosecond nuclear dynamics underlying the mapping phenomenon. DOI: 10.1103/PhysRevX.3.011017
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| 9. |
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| 10. |
- Lindblad, Andreas, et al.
(författare)
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Vibrational scattering anisotropy in O-2-dynamics beyond the Born-Oppenheimer approximation
- 2012
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Ingår i: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 14, s. 113018-
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Tidskriftsartikel (refereegranskat)abstract
- Born-Oppenheimer and Franck-Condon approximations are two major concepts in the interpretation of electronic excitations and modeling of spectroscopic data in the gas and condensed phases. We report large variations of the anisotropy parameter (beta) for the fully resolved vibrational sub-states of the X-2 Pi(g) electronic ground state of O-2(+) populated by participator resonant Auger decay following excitations of K-shell electrons into the sigma(star) resonance by monochromatic x-rays. Decay spectra for light polarization directions parallel and perpendicular to the electron detection axis recorded at four different excitation energies in the vicinity of the O 1s -> sigma(star) transition are presented. Breakdown of the Born-Oppenheimer approximation is for the first time selectively observed for the lower vibrational sub-states, where two quantum paths-resonant and direct-leading to the same final cationic state exist. The higher vibrational sub-states can only be populated by resonant photoemission; hence no interference between these channels can occur.
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