| 1. |
- Aad, G., et al.
(författare)
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- 2010
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swepub:Mat__t
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| 2. |
- Teslovich, Tanya M., et al.
(författare)
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Biological, clinical and population relevance of 95 loci for blood lipids
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 466:7307, s. 707-713
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Tidskriftsartikel (refereegranskat)abstract
- Plasma concentrations of total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol and triglycerides are among the most important risk factors for coronary artery disease (CAD) and are targets for therapeutic intervention. We screened the genome for common variants associated with plasma lipids in >100,000 individuals of European ancestry. Here we report 95 significantly associated loci (P<5 x 10(-8)), with 59 showing genome-wide significant association with lipid traits for the first time. The newly reported associations include single nucleotide polymorphisms (SNPs) near known lipid regulators (for example, CYP7A1, NPC1L1 and SCARB1) as well as in scores of loci not previously implicated in lipoprotein metabolism. The 95 loci contribute not only to normal variation in lipid traits but also to extreme lipid phenotypes and have an impact on lipid traits in three non-European populations (East Asians, South Asians and African Americans). Our results identify several novel loci associated with plasma lipids that are also associated with CAD. Finally, we validated three of the novel genes-GALNT2, PPP1R3B and TTC39B-with experiments in mouse models. Taken together, our findings provide the foundation to develop a broader biological understanding of lipoprotein metabolism and to identify new therapeutic opportunities for the prevention of CAD.
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| 3. |
- Brownstein, Catherine A., et al.
(författare)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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| 4. |
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| 5. |
- Buchhave, Lars A., et al.
(författare)
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An abundance of small exoplanets around stars with a wide range of metallicities
- 2012
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 486:7403, s. 375-377
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Tidskriftsartikel (refereegranskat)abstract
- The abundance of heavy elements (metallicity) in the photospheres of stars similar to the Sun provides a 'fossil' record of the chemical composition of the initial protoplanetary disk. Metal-rich stars are much more likely to harbour gas giant planets(1-4), supporting the model that planets form by accumulation of dust and ice particles(5). Recent ground-based surveys suggest that this correlation is weakened for Neptunian-sized planets(4,6-9). However, how the relationship between size and metallicity extends into the regime of terrestrial-sized exoplanets is unknown. Here we report spectroscopic metallicities of the host stars of 226 small exoplanet candidates discovered by NASA's Kepler mission(10), including objects that are comparable in size to the terrestrial planets in the Solar System. We find that planets with radii less than four Earth radii form around host stars with a wide range of metallicities (but on average a metallicity close to that of the Sun), whereas large planets preferentially form around stars with higher metallicities. This observation suggests that terrestrial planets may be widespread in the disk of the Galaxy, with no special requirement of enhanced metallicity for their formation.
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| 6. |
- Hudson, Lawrence N., et al.
(författare)
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The PREDICTS database : a global database of how local terrestrial biodiversity responds to human impacts
- 2014
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 4:24, s. 4701-4735
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Tidskriftsartikel (refereegranskat)abstract
- Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species' threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project - and avert - future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups - including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems - ). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.
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| 7. |
- Assimes, Themistocles L., et al.
(författare)
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Lack of Association Between the Trp719Arg Polymorphism in Kinesin-Like Protein-6 and Coronary Artery Disease in 19 Case-Control Studies
- 2010
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Ingår i: Journal of the American College of Cardiology. - : Elsevier BV. - 0735-1097. ; 56:19, s. 1552-1563
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Tidskriftsartikel (refereegranskat)abstract
- Objectives We sought to replicate the association between the kinesin-like protein 6 (KIF6) Trp719Arg polymorphism (rs20455), and clinical coronary artery disease (CAD). Background Recent prospective studies suggest that carriers of the 719Arg allele in KIF6 are at increased risk of clinical CAD compared with noncarriers. Methods The KIF6 Trp719Arg polymorphism (rs20455) was genotyped in 19 case-control studies of nonfatal CAD either as part of a genome-wide association study or in a formal attempt to replicate the initial positive reports. Results A total of 17,000 cases and 39,369 controls of European descent as well as a modest number of South Asians, African Americans, Hispanics, East Asians, and admixed cases and controls were successfully genotyped. None of the 19 studies demonstrated an increased risk of CAD in carriers of the 719Arg allele compared with noncarriers. Regression analyses and fixed-effects meta-analyses ruled out with high degree of confidence an increase of >= 2% in the risk of CAD among European 719Arg carriers. We also observed no increase in the risk of CAD among 719Arg carriers in the subset of Europeans with early-onset disease (younger than 50 years of age for men and younger than 60 years of age for women) compared with similarly aged controls as well as all non-European subgroups. Conclusions The KIF6 Trp719Arg polymorphism was not associated with the risk of clinical CAD in this large replication study. (J Am Coll Cardiol 2010;56:1552-63) (C) 2010 by the American College of Cardiology Foundation
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| 8. |
- Curtis, Bruce A., et al.
(författare)
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Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs
- 2012
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 492:7427, s. 59-65
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Tidskriftsartikel (refereegranskat)abstract
- Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote-eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have >21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host-and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph.
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| 9. |
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| 10. |
- Furberg, Helena, et al.
(författare)
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Genome-wide meta-analyses identify multiple loci associated with smoking behavior
- 2010
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 42:5, s. 134-441
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Tidskriftsartikel (refereegranskat)abstract
- Consistent but indirect evidence has implicated genetic factors in smoking behavior1,2. We report meta-analyses of several smoking phenotypes within cohorts of the Tobacco and Genetics Consortium (n = 74,053). We also partnered with the European Network of Genetic and Genomic Epidemiology (ENGAGE) and Oxford-GlaxoSmithKline (Ox-GSK) consortia to follow up the 15 most significant regions (n > 140,000). We identified three loci associated with number of cigarettes smoked per day. The strongest association was a synonymous 15q25 SNP in the nicotinic receptor gene CHRNA3 (rs1051730[A], b = 1.03, standard error (s.e.) = 0.053, beta = 2.8 x 10(-73)). Two 10q25 SNPs (rs1329650[G], b = 0.367, s. e. = 0.059, beta = 5.7 x 10(-10); and rs1028936[A], b = 0.446, s. e. = 0.074, beta = 1.3 x 10(-9)) and one 9q13 SNP in EGLN2 (rs3733829[G], b = 0.333, s. e. = 0.058, P = 1.0 x 10(-8)) also exceeded genome-wide significance for cigarettes per day. For smoking initiation, eight SNPs exceeded genome-wide significance, with the strongest association at a nonsynonymous SNP in BDNF on chromosome 11 (rs6265[C], odds ratio (OR) = 1.06, 95% confidence interval (Cl) 1.04-1.08, P = 1.8 x 10(-8)). One SNP located near DBH on chromosome 9 (rs3025343[G], OR = 1.12, 95% Cl 1.08-1.18, P = 3.6 x 10(-8)) was significantly associated with smoking cessation.
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| 11. |
- Lucas, W. E., et al.
(författare)
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Misaligned streamers around a Galactic Centre black hole from a single cloud's infall
- 2013
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Ingår i: Monthly Notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 1365-2966 .- 0035-8711. ; 433:1, s. 353-365
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Tidskriftsartikel (refereegranskat)abstract
- We follow the near radial infall of a prolate cloud on to a 4 x 10(6) M-circle dot supermassive black hole in the Galactic Centre using smoothed particle hydrodynamics. We show that a prolate cloud oriented perpendicular to its orbital plane naturally produces a spread in angular momenta in the gas which can translate into misaligned discs as is seen in the young stars orbiting Sagittarius A*. A turbulent or otherwise highly structured cloud is necessary to avoid cancelling too much angular momentum through shocks at closest approach. Our standard model of a 2 x 10(4) M-circle dot gas cloud brought about the formation of a disc within 0.3 pc from the black hole and a larger, misaligned streamer at 0.5 pc. A total of 1.5 x 10(4) M-circle dot of gas formed these structures. Our exploration of the simulation parameter space showed that when star formation occurred, it resulted in top-heavy initial mass functions with stars on eccentric orbits with semi-major axes 0.02-0.3 pc and inclinations following the gas discs and streamers. We suggest that the single event of an infalling prolate cloud can explain the occurrence of multiple misaligned discs of young stars.
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| 12. |
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| 13. |
- Ahlenius, Henrik, et al.
(författare)
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Adaptor Protein LNK Is a Negative Regulator of Brain Neural Stem Cell Proliferation after Stroke.
- 2012
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Ingår i: The Journal of Neuroscience : the official journal of the Society for Neuroscience. - 1529-2401. ; 32:15, s. 5151-5164
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Tidskriftsartikel (refereegranskat)abstract
- Ischemic stroke causes transient increase of neural stem and progenitor cell (NSPC) proliferation in the subventricular zone (SVZ), and migration of newly formed neuroblasts toward the damaged area where they mature to striatal neurons. The molecular mechanisms regulating this plastic response, probably involved in structural reorganization and functional recovery, are poorly understood. The adaptor protein LNK suppresses hematopoietic stem cell self-renewal, but its presence and role in the brain are poorly understood. Here we demonstrate that LNK is expressed in NSPCs in the adult mouse and human SVZ. Lnk(-/-) mice exhibited increased NSPC proliferation after stroke, but not in intact brain or following status epilepticus. Deletion of Lnk caused increased NSPC proliferation while overexpression decreased mitotic activity of these cells in vitro. We found that Lnk expression after stroke increased in SVZ through the transcription factors STAT1/3. LNK attenuated insulin-like growth factor 1 signaling by inhibition of AKT phosphorylation, resulting in reduced NSPC proliferation. Our findings identify LNK as a stroke-specific, endogenous negative regulator of NSPC proliferation, and suggest that LNK signaling is a novel mechanism influencing plastic responses in postischemic brain.
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| 14. |
- Andersen, M. R., et al.
(författare)
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Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88
- 2011
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 21:6, s. 885-897
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Tidskriftsartikel (refereegranskat)abstract
- The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compel additional exploration. We therefore undertook wholegenome sequencing of the acidogenic A. niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence, and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was used to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 Mb of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis supported up-regulation of genes associated with biosynthesis of amino acids that are abundant in glucoamylase A, tRNA-synthases, and protein transporters in the protein producing CBS 513.88 strain. Our results and data sets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi
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| 15. |
- Bécoulet, A., et al.
(författare)
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Science and technology research and development in support to ITER and the Broader Approach at CEA
- 2013
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 53:10
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Tidskriftsartikel (refereegranskat)abstract
- In parallel to the direct contribution to the procurement phase of ITER and Broader Approach, CEA has initiated research & development programmes, accompanied by experiments together with a significant modelling effort, aimed at ensuring robust operation, plasma performance, as well as mitigating the risks of the procurement phase. This overview reports the latest progress in both fusion science and technology including many areas, namely the mitigation of superconducting magnet quenches, disruption-generated runaway electrons, edge-localized modes (ELMs), the development of imaging surveillance, and heating and current drive systems for steady-state operation. The WEST (W Environment for Steady-state Tokamaks) project, turning Tore Supra into an actively cooled W-divertor platform open to the ITER partners and industries, is presented.
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| 16. |
- Bergman, Anders, et al.
(författare)
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Design of a wideband HVDC reference divider
- 2012
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Ingår i: Conference on Precision Electromagnetic Measurements, CPEM 2012. - : IEEE. ; , s. 207-208
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Konferensbidrag (refereegranskat)
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| 17. |
- Bergman, Anders, et al.
(författare)
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Metrology for high voltage direct current
- 2010
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Ingår i: CPEM Digest (Conference on Precision Electromagnetic Measurements). - 9781424467952 ; , s. 669-670
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Konferensbidrag (refereegranskat)abstract
- HVDC energy transmission is crucial for a successful uptake of renewable energy sources in the grid. A research program is described, intended to provide metrology support for the needs of HVDC energy transmission. This program will provide improvements for the present HVDC metrology infrastructure: accurate measurement of HVDC, determination of losses in HVDC systems, on-site power quality measurements at HVDC substations, and DC metering. It is a combined effort of 7 European national metrology institutes, one university and one industrial partner. © 2010 IEEE.
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| 18. |
- Braaten, E., et al.
(författare)
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Efimov physics in Li-6 atoms
- 2010
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Ingår i: Physical Review A - Atomic, Molecular, and Optical Physics. - 2469-9926 .- 2469-9934. ; 81:1
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Tidskriftsartikel (refereegranskat)abstract
- A new narrow three-atom loss resonance associated with an Efimov trimer crossing the three-atom threshold has recently been discovered in a many-body system of ultracold Li-6 atoms in the three lowest hyperfine spin states at a magnetic field near 895 G. O'Hara and coworkers have used measurements of the three-body recombination rate in this region to determine the complex three-body parameter associated with Efimov physics. Using this parameter as the input, we calculate the universal predictions for the spectrum of Efimov states and for the three-body recombination rate in the universal region above 600 G where all three scattering lengths are large. We predict an atom-dimer loss resonance at 672 +/- 2G associated with an Efimov trimer disappearing through an atom-dimer threshold. We also predict an interference minimum in the three-body recombination rate at 759 +/- 1G where the three-spin mixture may be sufficiently stable to allow experimental study of the many-body system.
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| 19. |
- Braaten, E., et al.
(författare)
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Renormalization in the three-body problem with resonant p-wave interactions
- 2012
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Ingår i: Physical Review A - Atomic, Molecular, and Optical Physics. - 2469-9926 .- 2469-9934. ; 86:1
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Tidskriftsartikel (refereegranskat)abstract
- Resonant p-wave interactions can be described by a minimal zero-range model defined by a truncated effective range expansion so that the only two-body interaction parameters are the inverse scattering volume 1/a(p) and the p-wave effective range r(p). This minimal model can be formulated as a local quantum field theory with a p-wave interaction between atom fields and a molecular field. In the two-atom sector, the model is renormalizable, but it has unphysical behavior at high energies because there are negative-probability states with momentum scale r(p). In the sector with three atoms, two of which are identical, renormalization in some parity and angular momentum channels involves an ultraviolet limit cycle, indicating asymptotic discrete scale invariance. The Efimov effect occurs in the unitary limit a(p)(-1/3),r(p) -> 0, but this limit is unphysical because there are low-energy states with negative probability. The minimal model can be of physical relevance only at energies small compared to the energy scale set by r(p) where the effects of negative-probability states are suppressed.
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| 20. |
- Hagen, G., et al.
(författare)
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Efimov Physics Around the Neutron-Rich Ca-60 Isotope
- 2013
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Ingår i: Physical Review Letters. - 1079-7114 .- 0031-9007. ; 111:13
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Tidskriftsartikel (refereegranskat)abstract
- We calculate the neutron-Ca-60 S-wave scattering phase shifts using state of the art coupled-cluster theory combined with modern ab initio interactions derived from chiral effective theory. Effects of three-nucleon forces are included schematically as density dependent nucleon-nucleon interactions. This information is combined with halo effective field theory in order to investigate the Ca-60-neutron-neutron system. We predict correlations between different three-body observables and the two-neutron separation energy of Ca-62. This provides evidence of Efimov physics along the calcium isotope chain. Experimental key observables that facilitate a test of our findings are discussed.
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| 21. |
- Hagen, P., et al.
(författare)
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Charge form factors of two-neutron halo nuclei in halo EFT
- 2013
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Ingår i: European Physical Journal A. - : Springer Science and Business Media LLC. - 1434-601X .- 1434-6001. ; 49:9, s. 1-13
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Tidskriftsartikel (refereegranskat)abstract
- We set up a formalism to calculate the charge form factors of two-neutron halo nuclei with S-wave neutron-core interactions in the framework of the halo effective field theory. The method is applied to some known and suspected halo nuclei. In particular, we calculate the form factors and charge radii relative to the core to leading order in the halo EFT and compare to experiments where they are available. Moreover, we investigate the general dependence of the charge radius on the core mass and the one-and two-neutron separation energies.
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| 22. |
- Hallstrom, J., et al.
(författare)
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Performance of a modular wideband 1000 kV HVDC reference divider
- 2014
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Ingår i: CPEM Digest (Conference on Precision Electromagnetic Measurements). - 9781479952052 ; , s. 782-783
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Konferensbidrag (refereegranskat)abstract
- This paper describes the performance of a wideband HVDC reference divider. The divider concept is a shielded modular divider and it is intended for traceable calibration of HVDC measuring systems up to 1000 kV in customers' laboratories. The first priority in the design was the accuracy of HVDC measurements. In addition, the divider was designed to have wide bandwidth, both to enable measurement of ripple voltages and to prevent damage during possible flashovers. © 2014 IEEE.
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| 23. |
- Hammer, H. W., et al.
(författare)
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Efimov physics in atom-dimer scattering of Li-6 atoms
- 2010
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Ingår i: Physical Review A - Atomic, Molecular, and Optical Physics. - 2469-9926 .- 2469-9934. ; 82:2
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Tidskriftsartikel (refereegranskat)abstract
- Li-6 atoms in the three lowest hyperfine states display universal properties when the S-wave scattering length between each pair of states is large. Recent experiments reported four pronounced features arising from Efimov physics in the atom-dimer relaxation rate, namely two resonances and two local minima. We use the universal effective-field theory to calculate the atom-dimer relaxation rate at zero temperature. Our results describe the four features qualitatively and imply there is a hidden local minimum. In the vicinity of the resonance at 685 G, we perform a finite temperature calculation which improves the agreement of theory and experiment. We conclude that finite temperature effects cannot be neglected in the analysis of the experimental data.
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| 24. |
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| 25. |
- Ladd, Brenton, et al.
(författare)
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Carbon isotopic signatures of soil organic matter correlate with leaf area index across woody biomes
- 2014
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Ingår i: Journal of Ecology. - : Wiley. - 0022-0477 .- 1365-2745. ; 102:6, s. 1606-1611
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Tidskriftsartikel (refereegranskat)abstract
- Leaf area index (LAI), a measure of canopy density, is a key variable for modelling and understanding primary productivity, and also water use and energy exchange in forest ecosystems. However, LAI varies considerably with phenology and disturbance patterns, so alternative approaches to quantifying stand-level processes should be considered. The carbon isotope composition of soil organic matter (C-13(SOM)) provides a time-integrated, productivity-weighted measure of physiological and stand-level processes, reflecting biomass deposition from seasonal to decadal time scales.Our primary aim was to explore how well LAI correlates with C-13(SOM) across biomes.Using a global data set spanning large environmental gradients in tropical, temperate and boreal forest and woodland, we assess the strength of the correlation between LAI and C-13(SOM); we also assess climatic variables derived from the WorldClim database.We found that LAI was strongly correlated with C-13(SOM), but was also correlated with Mean Temperature of the Wettest Quarter, Mean Precipitation of Warmest Quarter and Annual Solar Radiation across and within biomes.Synthesis. Our results demonstrate that C-13(SOM) values can provide spatially explicit estimates of leaf area index (LAI) and could therefore serve as a surrogate for productivity and water use. While C-13(SOM) has traditionally been used to reconstruct the relative abundance of C-3 versus C-4 species, the results of this study demonstrate that within stable C-3- or C-4-dominated biomes, C-13(SOM) can provide additional insights. The fact that LAI is strongly correlated to C-13(SOM) may allow for a more nuanced interpretation of ecosystem properties of palaeoecosystems based on palaeosol C-13 values.
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| 26. |
- 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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| 27. |
- Padamsee, Mahajabeen, et al.
(författare)
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The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction
- 2012
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 49:3, s. 217-226
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Tidskriftsartikel (refereegranskat)abstract
- Wallemia (Wallemiales, Wallemiomycetes) is a genus of xerophilic Fungi of uncertain phylogenetic position within Basidiomycota. Most commonly found as food contaminants, species of Wallemia have also been isolated from hypersaline environments. The ability to tolerate environments with reduced water activity is rare in Basidiomycota. We sequenced the genome of W. sebi in order to understand its adaptations for surviving in osmotically challenging environments, and we performed phylogenomic and ultrastructural analyses to address its systematic placement and reproductive biology. W. sebi has a compact genome (9.8Mb), with few repeats and the largest fraction of genes with functional domains compared with other Basidiomycota. We applied several approaches to searching for osmotic stress-related proteins. In silico analyses identified 93 putative osmotic stress proteins; homology searches showed the HOG (High Osmolarity Glycerol) pathway to be mostly conserved. Despite the seemingly reduced genome, several gene family expansions and a high number of transporters (549) were found that also provide clues to the ability of W. sebi to colonize harsh environments. Phylogenetic analyses of a 71-protein dataset support the position of Wallemia as the earliest diverging lineage of Agaricomycotina, which is confirmed by septal pore ultrastructure that shows the septal pore apparatus as a variant of the Tremella-type. Mating type gene homologs were identified although we found no evidence of meiosis during conidiogenesis, suggesting there may be aspects of the life cycle of W. sebi that remain cryptic.
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| 28. |
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| 29. |
- Padmanabhan, Sandosh, et al.
(författare)
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Genome-Wide Association Study of Blood Pressure Extremes Identifies Variant near UMOD Associated with Hypertension
- 2010
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Ingår i: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7404. ; 6:10
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Tidskriftsartikel (refereegranskat)abstract
- Hypertension is a heritable and major contributor to the global burden of disease. The sum of rare and common genetic variants robustly identified so far explain only 1%-2% of the population variation in BP and hypertension. This suggests the existence of more undiscovered common variants. We conducted a genome-wide association study in 1,621 hypertensive cases and 1,699 controls and follow-up validation analyses in 19,845 cases and 16,541 controls using an extreme case-control design. We identified a locus on chromosome 16 in the 59 region of Uromodulin (UMOD; rs13333226, combined P value of 3.6x10(-11)). The minor G allele is associated with a lower risk of hypertension (OR [95% CI]: 0.87 [0.84-0.91]), reduced urinary uromodulin excretion, better renal function; and each copy of the G allele is associated with a 7.7% reduction in risk of CVD events after adjusting for age, sex, BMI, and smoking status (H.R. = 0.923, 95% CI 0.860-0.991; p = 0.027). In a subset of 13,446 individuals with estimated glomerular filtration rate (eGFR) measurements, we show that rs13333226 is independently associated with hypertension (unadjusted for eGFR: 0.89 [0.83-0.96], p = 0.004; after eGFR adjustment: 0.89 [0.83-0.96], p = 0.003). In clinical functional studies, we also consistently show the minor G allele is associated with lower urinary uromodulin excretion. The exclusive expression of uromodulin in the thick portion of the ascending limb of Henle suggests a putative role of this variant in hypertension through an effect on sodium homeostasis. The newly discovered UMOD locus for hypertension has the potential to give new insights into the role of uromodulin in BP regulation and to identify novel drugable targets for reducing cardiovascular risk.
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| 30. |
- RYBERG, EMIL, 1987, et al.
(författare)
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Constraining low-energy proton capture on beryllium-7 through charge radius measurements
- 2014
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Ingår i: European Physical Journal A. - : Springer Science and Business Media LLC. - 1434-601X .- 1434-6001. ; 50:11, s. 170-182
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we point out that a measurement of the charge radius of boron-8 provides indirect access to the S-factor for radiative proton capture on beryllium-7 at low energies. We use leading-order halo effective field theory to explore this correlation and we give a relation between the charge radius and the S-factor. Furthermore, we present important technical aspects relevant to the renormalization of point-like P -wave interactions in the presence of a repulsive Coulomb interaction.
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| 31. |
- RYBERG, EMIL, 1987, et al.
(författare)
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Effective field theory for proton halo nuclei
- 2014
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Ingår i: Physical Review C - Nuclear Physics. - 2469-9985 .- 2469-9993. ; 89:1
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Tidskriftsartikel (refereegranskat)abstract
- We use halo effective field theory to analyze the universal features of proton halo nuclei bound due to a large S-wave scattering length. Our work provides a fully field-theoretical treatment of bound halo nuclei in the presence of a repulsive Coulomb interaction. With a Lagrangian built from effective core and valence-proton fields, we derive a leading-order expression for the charge form factor. Within the same framework we also calculate the radiative proton capture cross section. We present general results at leading order that can be applied to any one-proton halo system bound in a relative S wave. We illustrate the method by studying the excited 1/2(+) state of fluorine 17, for which we give results for the charge radius and the astrophysical S factor.
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| 32. |
- Timmermans, Anne, et al.
(författare)
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Endometrial Thickness Measurement for Detecting Endometrial Cancer in Women With Postmenopausal Bleeding A Systematic Review and Meta-Analysis
- 2010
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Ingår i: Obstetrics and Gynecology. - 1873-233X. ; 116:1, s. 160-167
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Forskningsöversikt (refereegranskat)abstract
- OBJECTIVE: To estimate the accuracy of endometrial thickness measurement in the detection of endometrial cancer among women with postmenopausal bleeding with individual patient data using different meta-analytic strategies. DATA SOURCES: Original data sets of studies detected after reviewing the included studies of three previous reviews on this subject. An additional literature search of published articles using MEDLINE databases was preformed from January 2000 to December 2006 to identify articles reporting on endometrial carcinoma and sonographic endometrial thickness measurement in women with postmenopausal bleeding. METHODS OF STUDY SELECTION: We identified 90 studies reporting on endometrial thickness measurements and endometrial carcinoma in women with postmenopausal bleeding. TABULATION, INTEGRATION, AND RESULTS: We contacted 79 primary investigators to obtain the individual patient data of their reported studies, of which 13 could provide data. Data on 2,896 patients, of which 259 had carcinoma, were included. Several approaches were used in the analyses of the acquired data. First, we performed receiver operator characteristics (ROC) analysis per study, resulting in a summary area under the ROC curve (AUC) calculated as a weighted mean of AUCs from original studies. Second, individual patient data were pooled and analyzed with ROC analyses irrespective of study with standardization of distributional differences across studies using multiples of the median and by random effects logistic regression. Finally, we also used a two-stage procedure, calculating sensitivities and specificities for each study and using the bivariate random effects model to estimate summary estimates for diagnostic accuracy. This resulted in rather comparable ROC curves with AUCs varying between 0.82 and 0.84 and summary estimates for sensitivity and specificity located along these curves. These curves indicated a lower AUC than previously reported meta-analyses using conventional techniques. CONCLUSION: Previous meta-analyses on endometrial thickness measurement probably have overestimated its diagnostic accuracy in the detection of endometrial carcinoma. We advise the use of cutoff level of 3 mm for exclusion of endometrial carcinoma in women with postmenopausal bleeding. (Obstet Gynecol 2010;116:160-7)
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| 33. |
- Waluk, Dominik P., et al.
(författare)
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Mammalian Fatty Acid Amides of the Brain and CNS
- 2014
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Ingår i: Omega-3 Fatty Acids in Brain and Neurological Health. - London : Academic Press Ltd-Elsevier Science Ltd. - 9780124105478 - 9780124105270 ; , s. 87-107
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Bokkapitel (refereegranskat)
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