| 1. |
- Kanai, M, et al.
(författare)
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- 2023
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swepub:Mat__t
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| 2. |
- 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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| 3. |
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| 6. |
- Hait, A. S., et al.
(författare)
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Defects in LC3B2 and ATG4A underlie HSV2 meningitis and reveal a critical role for autophagy in antiviral defense in humans
- 2020
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Ingår i: Science Immunology. - : American Association for the Advancement of Science (AAAS). - 2470-9468. ; 5:54
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Tidskriftsartikel (refereegranskat)abstract
- Recurrent herpesvirus infections can manifest in different forms of disease, including cold sores, genital herpes, and encephalitis. There is an incomplete understanding of the genetic and immunological factors conferring susceptibility to recurrent herpes simplex virus 2 (HSV2) infection in the central nervous system (CNS). Here, we describe two adult patients with recurrent HSV2 lymphocytic Mollaret's meningitis that each carry a rare monoallelic variant in the autophagy proteins ATG4A or LC3B2. HSV2-activated autophagy was abrogated in patient primary fibroblasts, which also exhibited significantly increased viral replication and enhanced cell death. HSV2 antigen was captured in autophagosomes of infected cells, and genetic inhibition of autophagy by disruption of autophagy genes, including ATG4A and LC3B2, led to enhanced viral replication and cell death in primary fibroblasts and a neuroblastoma cell line. Activation of autophagy by HSV2 was sensitive to ultraviolet (UV) irradiation of the virus and inhibited in the presence of acyclovir, but HSV2-induced autophagy was independent of the DNA-activated STING pathway. Reconstitution of wild-type ATG4A and LC3B2 expression using lentiviral gene delivery or electroporation of in vitro transcribed mRNA into patient cells restored virus-induced autophagy and the ability to control HSV2 replication. This study describes a previously unknown link between defective autophagy and an inborn error of immunity that can lead to increased susceptibility to HSV2 infection, suggesting an important role for autophagy in antiviral immunity in the CNS.
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| 7. |
- Mikkelsen, Tarjei S, et al.
(författare)
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Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7141, s. 167-177
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Tidskriftsartikel (refereegranskat)abstract
- We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.
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| 8. |
- Hartoog, O. E., et al.
(författare)
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VLT/X-Shooter spectroscopy of the afterglow of the Swift GRB 130606A Chemical abundances and reionisation at z similar to 6
- 2015
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 580
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Tidskriftsartikel (refereegranskat)abstract
- Context: The reionisation of the Universe is a process that is thought to have ended around z similar to 6, as inferred from spectroscopy of distant bright background sources, such as quasars (QSO) and gamma-ray burst (GRB) afterglows. Furthermore, spectroscopy of a GRB afterglow provides insight in its host galaxy, which is often too dim and distant to study otherwise.Aims: For the Swift GRB 130606A at z = 5.913 we have obtained a high S/N spectrum covering the full optical and near-IR wavelength region at intermediate spectral resolution with VLT/X-Shooter. We aim to measure the degree of ionisation of the intergalactic medium (IGM) between z = 5.02-5.84 and to study the chemical abundance pattern and dust content of its host galaxy.Methods: We estimated the UV continuum of the GRB afterglow using a power-law extrapolation, then measured the flux decrement due to absorption at Ly alpha,beta, and gamma wavelength regions. Furthermore, we fitted the shape of the red damping wing of Lya. The hydrogen and metal absorption lines formed in the host galaxy were fitted with Voigt profiles to obtain column densities. We investigated whether ionisation corrections needed to be applied.Results: Our measurements of the Ly alpha-forest optical depth are consistent with previous measurements of QSOs, but have a much smaller uncertainty. The analysis of the red damping wing yields a neutral fraction x(HI) < 0.05 (3 sigma). We obtain column density measurements of H, Al, Si, and Fe; for C, O, S and Ni we obtain limits. The ionisation due to the GRB is estimated to be negligible (corrections < 0.03 dex), but larger corrections may apply due to the pre-existing radiation field (up to 0.4 dex based on sub-DLA studies). Assuming that [Si/Fe] = +0.79 +/- 0.13 is due to dust depletion, the dust-to-metal ratio is similar to the Galactic value.Conclusions: Our measurements confirm that the Universe is already predominantly ionised over the redshift range probed in this work, but was slightly more neutral at z > 5.6. GRBs are useful probes of the ionisation state of the IGM in the early Universe, but because of internal scatter we need a larger statistical sample to draw robust conclusions. The high [Si/Fe] in the host can be due to dust depletion, a-element enhancement, or a combination of both. The very high value of [Al/Fe] = 2.40 +/- 0.78 might be due to a proton capture process and is probably connected to the stellar population history. We estimate the host metallicity to be -1.7 < [M/H] < -0.9 (2%-13% of solar).
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| 9. |
- Mikkelsen, D.R, et al.
(författare)
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Assessment of Transport in NCSX
- 2007
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Ingår i: Fusion Science and Technology. ; 51, s. 166-180
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Tidskriftsartikel (refereegranskat)abstract
- We explore whether the energy confinement and planned heating in the National Compact Stellarator Experiment (NCSX) are sufficient to test magnetohydrodynamic (MHD) stability limits, and whether the configuration is sufficiently quasi-axisymmetric to reduce the neoclassical ripple transport to low levels, thereby allowing tokamak-like transport. A zero-dimensional model with fixed profile shapes is related to global energy confinement scalings for stellarators and tokamaks, neoclassical transport properties are assessed with the DKES, NEO, and NCLASS codes, and a power balance code is used to predict temperature profiles. Reaching the NCSX goal of = 4% at low collisionality will require HISS-95 = 3, which is higher than the best achieved in present stellarators. However, this level of confinement is actually ~10% lower than that predicted by the ITER-97P tokamak L-mode scaling. By operating near the stellarator density limit, the required HISS-95 is reduced by 35%. The high degree of quasi-axisymmetry of the configuration and the self-consistent "ambipolar" electric field reduce the neoclassical ripple transport to a small fraction of the neoclassical axisymmetric transport. A combination of neoclassical and anomalous transport models produces pressure profile shapes that are within the range of those used to study the MHD stability of NCSX. We find that = 4% plasmas are "neoclassically accessible" and are compatible with large levels of anomalous transport in the plasma periphery.
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| 10. |
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| 11. |
- Fischer, R, et al.
(författare)
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Towards a transnational system of supersites for forest monitoring and research in Europe - an overview on present state and future recommendations
- 2011
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Ingår i: IForest. - : Italian Society of Sivilculture and Forest Ecology (SISEF). - 1971-7458. ; 4:1, s. 167-171
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Tidskriftsartikel (refereegranskat)abstract
- Science based approaches in addressing future risks and challenges for forests require close collaboration among the communities operating different monitoring and research networks as well as experts in process and large-scale modelling. Results of the COST FP0903 conference which took place in October 2010 in Rome, reveal valuable results from different European forest monitoring and research networks. However, the need for closer integration of these activities is obvious. In this paper, representatives from major European networks recommend a new approach for forest monitoring and research in Europe, based on a reasonable number of highly instrumented "supersites" and a larger number of intensive monitoring plots linked to these. This system needs to be built on existing infrastructures but requires increased coordination, harmonisation and a joint long term platform for data exchange and modelling.
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| 12. |
- Fletcher, Tim D., et al.
(författare)
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SUDS, LID, BMPs, WSUD and more : The evolution and application of terminology surrounding urban drainage
- 2015
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Ingår i: Urban Water Journal. - 1573-062X. ; 12:7, s. 525-542
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Tidskriftsartikel (refereegranskat)abstract
- The management of urban stormwater has become increasingly complex over recent decades. Consequently, terminology describing the principles and practices of urban drainage has become increasingly diverse, increasing the potential for confusion and miscommunication. This paper documents the history, scope, application and underlying principles of terms used in urban drainage and provides recommendations for clear communication of these principles. Terminology evolves locally and thus has an important role in establishing awareness and credibility of new approaches and contains nuanced understandings of the principles that are applied locally to address specific problems. Despite the understandable desire to have a 'uniform set of terminology', such a concept is flawed, ignoring the fact that terms reflect locally shared understanding. The local development of terminology thus has an important role in advancing the profession, but authors should facilitate communication between disciplines and between regions of the world, by being explicit and accurate in their application. © 2014 © The work of Tim D. Fletcher is Crown copyright in the Commonwealth of Australia 2014, University of Melbourne. The work of Danielle Dagenais is Copyright of the Crown in Canada 2014, University of Montreal. The work of William Shuster was authored as part of his official duties as an Employee of the United States Government and is therefore a work of the United States Government. In accordance with 17 USC. 105, no copyright protection is available for such works under US Law. William F. Hunt, Richard Ashley, David Butler, Scott Arthur, Sam Trowsdale, Sylvie Barraud, Annette Semadeni-Davies, Jean-Luc Bertrand-Krajewski, Peter Steen Mikkelsen, Gilles Rivard, Mathias Uhl and Maria Viklander hereby waive their right to assert copyright, but not their right to be named as co-authors in the article.
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| 13. |
- Harrington, S. D., et al.
(författare)
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Electronic structure of epitaxial half-Heusler Co1-xNixTiSb across the semiconductor to metal transition
- 2018
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Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 113:9
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Tidskriftsartikel (refereegranskat)abstract
- Here, we report on the growth, electronic, and surface properties of the electron-doped half-Heusler series Co1-xNixTiSb (001) grown by molecular beam epitaxy. High-quality epitaxial growth of thin films is achieved on InP (001) substrates using an InAlAs buffer layer for all nickel concentrations. The semiconductor to metal transition as a function of substitutional alloying was examined using electrical transport, Seebeck measurements, and angle-resolved photoemission spectroscopy (ARPES). Temperature-dependent electrical transport measurements of films with composition x ≤ 0.1 exhibit thermally activated behavior while x > 0.1 exhibit metallic behavior. Smooth, highly ordered film surfaces can be achieved following ex-situ transfer of the films and subsequent desorption of a sacrificial, protective antimony capping layer. Using this transfer technique, ARPES experiments were performed to investigate the effects of nickel alloying on the electronic band structure. An electron pocket is observed below the Fermi level at the bulk X point for compositions x > 0.1, in accordance with the crossover from semiconducting to metallic behavior observed in the transport measurements.
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| 14. |
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| 15. |
- Kennedy, S. M., et al.
(författare)
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Characterizing the geometry of InAs nanowires using mirror electron microscopy
- 2012
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Ingår i: Nanotechnology. - : IOP Publishing. - 0957-4484 .- 1361-6528. ; 23:12
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Tidskriftsartikel (refereegranskat)abstract
- Mirror electron microscopy (MEM) imaging of InAs nanowires is a non-destructive electron microscopy technique where the electrons are reflected via an applied electric field before they reach the specimen surface. However strong caustic features are observed that can be non-intuitive and difficult to relate to nanowire geometry and composition. Utilizing caustic imaging theory we can understand and interpret MEM image contrast, relating caustic image features to the properties and parameters of the nanowire. This is applied to obtain quantitative information, including the nanowire width via a through-focus series of MEM images.
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| 16. |
- Lorek, Eleonora, et al.
(författare)
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High-Order Harmonic Generation and Plasmonics
- 2015
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Ingår i: Nano-Structures for Optics and Photonics : Optical Strategies for Enhancing Sensing, Imaging, Communication and Energy Conversion - Optical Strategies for Enhancing Sensing, Imaging, Communication and Energy Conversion. - Dordrecht : Springer Netherlands. - 9789401791328 - 9789401791335 ; , s. 531-531
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Bokkapitel (refereegranskat)abstract
- Attosecond pulses allow for imaging of very fast processes, like electron dynamics. Stockman et al. suggested to use these pulses in connection with a Photoemission electron microscope (PEEM) to study the ultrafast dynamics of plasmons (Stockman et al. Nat Photonics 1:539–544, 2007). For efficient plasmon studies, the repetition rate of the attosecond pulses used needs to be higher than a few kHz (Mikkelsen et al. Rev Sci Instrum 80:123703, 2009). Attosecond pulses are produced in a process called high-order harmonic generation (HHG) (Paul et al. Science 292(5522):1689–1692, 2001; Ferray et al. J Phys B At Mol Opt Phys 21:L31–L35, 1988). In HHG, a strong laser field allows an electron to tunnel out, get accelerated and recombine with a high kinetic energy resulting in extreme ultraviolet attosecond pulses. The large intensity needed to drive the process normally limits the repetition rate of the laser to a few kHz. Using a tight focusing scheme (Heyl et al. Phys Rev Lett 107:033903, 2011; Vernaleken et al. Opt Lett 36:3428–3430, 2011), we, however, generate harmonics at a repetition rate of 200 kHz, both with a commercial turn-key laser and with an advanced laser system. Suitable nanostructures for a strong field enhancement are produced in-house and the field enhancement is studied with PEEM in a non-time resolved manner. With high-order harmonics produced at a high repetition rate, we hope to be able to follow also the ultrafast dynamics of plasmons in these structures (Mårsell et al. Ann der Phys 525:162–170, 2013).
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| 19. |
- A. B. Marçal, L., et al.
(författare)
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Spatially resolved structural and chemical properties of the white layer in machined Inconel 718 super alloy
- 2024
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Ingår i: Materials and Design. - 0264-1275. ; 239
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Tidskriftsartikel (refereegranskat)abstract
- Inconel 718 is one type of nickel-based alloy used for a large range of applications, including gas turbines and aeroengines components. Although mechanical and thermodynamic properties of this material have been deeply studied in the past years, a method able to investigate local properties of the thin white layer formed on the alloy surface after machining remains challenging. Here, a 90 nm X-ray beam is used to probe the local strain, crystal orientation, and chemical composition of grains in the white layer. Data reveals mosaicity induced by the tool during machining. The high spatial resolution, combined with crystal lattice sensitivity, shows that the average grain size is around 30 nm throughout the white layer, while the strain is anisotropic nearest to the surface. Results provide new insights on the basic properties of the white layer in super alloys, revealing important information about the impact of finish machining which might help to explain fatigue and cracking formation on these materials during their usage phase.
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| 20. |
- Aidas, Kestutis, et al.
(författare)
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The Dalton quantum chemistry program system
- 2014
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Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 4:3, s. 269-284
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Tidskriftsartikel (refereegranskat)abstract
- Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from for a number of UNIX platforms.
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| 21. |
- Benter, S., et al.
(författare)
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2D electron gas formation on InAs wurtzite nanosheet surfaces
- 2024
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Ingår i: Applied Physics Letters. - 0003-6951. ; 124:15
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Tidskriftsartikel (refereegranskat)abstract
- The two-dimensional electron gas (2DEG) that forms on a semiconductor surface can be used to explore a variety of phenomena in quantum physics and plays an important role in nanoscale electronics, such as transistors. Controlling its formation is, thus, relevant. Using angle-resolved photoemission spectroscopy (ARPES) and accumulating the signal over many nanocrystals, we find that on clean InAs nanosheets with non-polar surfaces and wurtzite (WZ) crystal structures, a 2DEG can be observed at the Γ-point. We suggest that the step morphology on the WZ InAs specimens facilitates the appearance of the electron gas, since previous studies on InAs nanowire surfaces with the same crystal facet and a similar defect density did not exhibit a 2DEG. Subsequently, bismuth deposition leads to the disappearance of the 2DEG as well as a shift of the valence band. This is in contrast to previous observations on InAs surfaces, in which metal deposition would lead to the formation of a 2DEG. The control of the 2DEG with the addition of Bi atoms is relevant for applications of InAs nanosheets in quantum technologies. This study also illustrates that ARPES accumulated over several 2D materials oriented randomly around their normal axis can provide valuable information on their band structure with a fast turnover and low irradiation.
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| 22. |
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| 23. |
- Borga, M, et al.
(författare)
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Structure and dynamics of Na adsorption on Al(100)
- 2002
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Ingår i: 7th International Conference on Nanometer-Scale Science and Technology and 21st European Conference on Surface Science.
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Konferensbidrag (refereegranskat)abstract
- The adsorption of 0.2 monolayers (ML) of Na on Al(100) has been studied both experimentally, using low energy electron diffraction (LEED) and high resolution core level spectroscopy (HRCLS), and theoretically, using density functional theory (DFT). Two ordered phases are found: Islands of c (2×2) symmetry with Na atoms occupying four-fold hollow sites result from low temperature deposition and a (√5×√5)R27° structure with Na in surface substitutional sites is formed by annealing of the low temperature island structure at 300 K and subsequent cooling below 230 K. The (√5×√5)R27° structure undergoes a reversible order-disorder phase transition at ~230 K. To investigate this phase transition further, we performed additional DFT calculations for a wide range of coverages (from 0.0625 to 0.5 ML), for adsorption in both hollow and substitutional sites, from which we extract interaction energies which are used in a lattice gas Monte Carlo simulations
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| 24. |
- Bronden, A., et al.
(författare)
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Glucose-lowering effects and mechanisms of the bile acid-sequestering resin sevelamer
- 2018
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Ingår i: Diabetes Obesity & Metabolism. - : Wiley. - 1462-8902 .- 1463-1326. ; 20:7, s. 1623-1631
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Tidskriftsartikel (refereegranskat)abstract
- Aims Sevelamer, a non-absorbable amine-based resin used for treatment of hyperphosphataemia, has been demonstrated to have a marked bile acid-binding potential alongside beneficial effects on lipid and glucose metabolism. The aim of this study was to investigate the glucose-lowering effect and mechanism(s) of sevelamer in patients with type 2 diabetes. Materials and Methods In this double-blinded randomized controlled trial, we randomized 30 patients with type 2 diabetes to sevelamer (n = 20) or placebo (n = 10). Participants were subjected to standardized 4-hour liquid meal tests at baseline and after 7 days of treatment. The main outcome measure was plasma glucagon-like peptide-1 excursions as measured by area under the curve. In addition, blood was sampled for measurements of glucose, lipids, glucose-dependent insulinotropic polypeptide, C-peptide, glucagon, fibroblast growth factor-19, cholecystokinin and bile acids. Assessments of gastric emptying, resting energy expenditure and gut microbiota composition were performed. Results Sevelamer elicited a significant placebo-corrected reduction in plasma glucose with concomitant reduced fibroblast growth factor-19 concentrations, increased de novo synthesis of bile acids, a shift towards a more hydrophilic bile acid pool and increased lipogenesis. No glucagon-like peptide-1-mediated effects on insulin, glucagon or gastric emptying were evident, which points to a limited contribution of this incretin hormone to the glucose-lowering effect of sevelamer. Furthermore, no sevelamer-mediated effects on gut microbiota composition or resting energy expenditure were observed. Conclusions Sevelamer reduced plasma glucose concentrations in patients with type 2 diabetes by mechanisms that seemed to involve decreased intestinal and hepatic bile acid-mediated farnesoid X receptor activation.
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