| 1. |
- Kanai, M, et al.
(författare)
-
- 2023
-
swepub:Mat__t
|
|
| 2. |
- Campbell, PJ, et al.
(författare)
-
Pan-cancer analysis of whole genomes
- 2020
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
-
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.
|
|
| 3. |
|
|
| 4. |
|
|
| 5. |
|
|
| 6. |
- Hait, A. S., et al.
(författare)
-
Defects in LC3B2 and ATG4A underlie HSV2 meningitis and reveal a critical role for autophagy in antiviral defense in humans
- 2020
-
Ingår i: Science Immunology. - : American Association for the Advancement of Science (AAAS). - 2470-9468. ; 5:54
-
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.
|
|
| 7. |
- Mikkelsen, Tarjei S, et al.
(författare)
-
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
- 2007
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7141, s. 167-177
-
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.
|
|
| 8. |
- Hartoog, O. E., et al.
(författare)
-
VLT/X-Shooter spectroscopy of the afterglow of the Swift GRB 130606A Chemical abundances and reionisation at z similar to 6
- 2015
-
Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 580
-
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).
|
|
| 9. |
- Mikkelsen, D.R, et al.
(författare)
-
Assessment of Transport in NCSX
- 2007
-
Ingår i: Fusion Science and Technology. ; 51, s. 166-180
-
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.
|
|
| 10. |
|
|
| 11. |
- Fischer, R, et al.
(författare)
-
Towards a transnational system of supersites for forest monitoring and research in Europe - an overview on present state and future recommendations
- 2011
-
Ingår i: IForest. - : Italian Society of Sivilculture and Forest Ecology (SISEF). - 1971-7458. ; 4:1, s. 167-171
-
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.
|
|
| 12. |
- Fletcher, Tim D., et al.
(författare)
-
SUDS, LID, BMPs, WSUD and more : The evolution and application of terminology surrounding urban drainage
- 2015
-
Ingår i: Urban Water Journal. - 1573-062X. ; 12:7, s. 525-542
-
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.
|
|
| 13. |
- Harrington, S. D., et al.
(författare)
-
Electronic structure of epitaxial half-Heusler Co1-xNixTiSb across the semiconductor to metal transition
- 2018
-
Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 113:9
-
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.
|
|
| 14. |
|
|
| 15. |
- Kennedy, S. M., et al.
(författare)
-
Characterizing the geometry of InAs nanowires using mirror electron microscopy
- 2012
-
Ingår i: Nanotechnology. - : IOP Publishing. - 0957-4484 .- 1361-6528. ; 23:12
-
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.
|
|
| 16. |
- Lorek, Eleonora, et al.
(författare)
-
High-Order Harmonic Generation and Plasmonics
- 2015
-
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
-
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).
|
|
| 17. |
|
|
| 18. |
|
|
| 19. |
- A. B. Marçal, L., et al.
(författare)
-
Spatially resolved structural and chemical properties of the white layer in machined Inconel 718 super alloy
- 2024
-
Ingår i: Materials and Design. - 0264-1275. ; 239
-
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.
|
|
| 20. |
- Aidas, Kestutis, et al.
(författare)
-
The Dalton quantum chemistry program system
- 2014
-
Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 4:3, s. 269-284
-
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.
|
|
| 21. |
- Benter, S., et al.
(författare)
-
2D electron gas formation on InAs wurtzite nanosheet surfaces
- 2024
-
Ingår i: Applied Physics Letters. - 0003-6951. ; 124:15
-
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.
|
|
| 22. |
|
|
| 23. |
- Borga, M, et al.
(författare)
-
Structure and dynamics of Na adsorption on Al(100)
- 2002
-
Ingår i: 7th International Conference on Nanometer-Scale Science and Technology and 21st European Conference on Surface Science.
-
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
|
|
| 24. |
- Bronden, A., et al.
(författare)
-
Glucose-lowering effects and mechanisms of the bile acid-sequestering resin sevelamer
- 2018
-
Ingår i: Diabetes Obesity & Metabolism. - : Wiley. - 1462-8902 .- 1463-1326. ; 20:7, s. 1623-1631
-
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.
|
|
| 25. |
|
|
| 26. |
|
|
| 27. |
- de Graan, Anne-Joy M., et al.
(författare)
-
Influence of Polymorphic OATP1B-Type Carriers on the Disposition of Docetaxel
- 2012
-
Ingår i: Clinical Cancer Research. - 1078-0432 .- 1557-3265. ; 18:16, s. 4433-4440
-
Tidskriftsartikel (refereegranskat)abstract
- Purpose: Docetaxel is extensively metabolized by CYP3A4 in the liver but mechanisms by which the drug is taken up into hepatocytes remain poorly understood. We hypothesized that (i) liver uptake of docetaxel is mediated by the polymorphic solute carriers OATP1B1 and OATP1B3 and (ii) inherited genetic defects in this process may impair systemic drug elimination.Experimental Design: Transport of docetaxel was studied in vitro using various cell lines stably transfected with OATP1B1*1A (wild-type), OATP1B1*5 [c.521T>C (V174A); rs4149056], OATP1B3, or the mouse transporter Oatp1b2. Docetaxel clearance was evaluated in wild-type and Oatp1b2-knockout mice as well as in two cohorts of patients with multiple variant transporter genotypes (n = 213).Results: Docetaxel was found to be a substrate for OATP1B1, OATP1B3, and Oatp1b2 but was not transported by OATP1B1*5. Deficiency of Oatp1b2 in mice was associated with an 18-fold decrease in docetaxel clearance (P = 0.0099), which was unrelated to changes in intrinsic metabolic capacity in mouse liver microsomes. In patients, however, none of the studied common reduced function variants in OATP1B1 or OATP1B3 were associated with docetaxel clearance (P > 0.05).Conclusions: The existence of at least two potentially redundant uptake transporters in the human liver with similar affinity for docetaxel supports the possibility that functional defects in both of these proteins may be required to confer substantially altered disposition phenotypes. In view of the established exposure-toxicity relationships for docetaxel, we suggest that caution is warranted if docetaxel has to be administered together with agents that potently inhibit both OATP1B1 and OATP1B3.
|
|
| 28. |
- Dzhigaev, D., et al.
(författare)
-
Bragg coherent x-ray diffractive imaging of a single indium phosphide nanowire
- 2016
-
Ingår i: Journal of Optics. - : IOP Publishing. - 2040-8978 .- 2040-8986. ; 18:6
-
Tidskriftsartikel (refereegranskat)abstract
- Three-dimensional (3D) Bragg coherent x-ray diffractive imaging (CXDI) with a nanofocused beam was applied to quantitatively map the internal strain field of a single indium phosphide nanowire. The quantitative values of the strain were obtained by pre-characterization of the beam profile with transmission ptychography on a test sample. Our measurements revealed the 3D strain distribution in a region of 150 nm below the catalyst Au particle. We observed a slight gradient of the strain in the range of 0.6% along the [111] growth direction of the nanowire. We also determined the spatial resolution in our measurements to be about 10 nm in the direction perpendicular to the facets of the nanowire. The CXDI measurements were compared with the finite element method simulations and show a good agreement with our experimental results. The proposed approach can become an effective tool for in operando studies of the nanowires.
|
|
| 29. |
- Dzhigaev, D, et al.
(författare)
-
Three-dimensional coherent x-ray diffraction imaging of ferroelastic domains in single CsPbBr3 perovskite nanoparticles
- 2021
-
Ingår i: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 23:6
-
Tidskriftsartikel (refereegranskat)abstract
- Metal halide perovskites attract significant interest due to their remarkable performance in optoelectronic devices. However, the gap in understanding the relationship between their nanoscale structure and properties limits their application towards novel devices. In this work, twinned ferroelastic domains in single 500 nm CsPbBr3 particles are studied with 3D Bragg coherent x-ray diffraction imaging. A preferential double-domain structure is revealed in four identical particles, with one domain oriented along the [110] and the other along the [002] direction. The particles exhibit similar scattering volume ratios of 0.12 0.026 between twin phases, suggesting the possibility of a deterministic formation process. The domains exhibit a difference in lattice tilt of 0.59 degrees, in excellent agreement with calculations of the lattice mismatch at the (112) twin boundary. These results provide important insights both for the fundamental understanding of ferroelastic nanoscale materials and for the performance improvement of perovskite-based devices. Moreover, this work paves the way towards real-time imaging of the domain dynamics in ferroic systems.
|
|
| 30. |
- Eriksson, Eva, 1973-, et al.
(författare)
-
Water management in cities of the future using emission control strategies for priority hazardous substances
- 2011
-
Ingår i: Water Science and Technology. - : IWA Publishing. - 0273-1223 .- 1996-9732. ; 64:10, s. 2109-2118
-
Tidskriftsartikel (refereegranskat)abstract
- Cities of the future face challenges with respect to the quantity and quality of water resources, and multiple managerial options need to be considered in order to safeguard urban surface water quality. In a recently completed project on “Source Control Options for Reducing Emissions of Priority Pollutants” (ScorePP), seven emission control strategies (ECS) have been developed and tested on a semi-hypothetical case city (SHCCA) for selected European priority pollutants (PPs). The SHCCA approach was chosen to facilitate transparency, to mitigate data gaps and to decrease the level of uncertainty in the results. The selected PPs differ in their uses and environmental fate and therefore accumulate in different urban environmental compartment. To achieve the required reduction in PP levels in urban waters the full implementation of existing EU regulation is essential and appropriate combinations of managerial and technological options (source control and treatment) can be highly relevant.
|
|
| 31. |
- Fowler, D., et al.
(författare)
-
Atmospheric composition change : Ecosystems-Atmosphere interactions
- 2009
-
Ingår i: Atmospheric Environment. - : Elsevier BV. - 1352-2310 .- 1873-2844. ; 43:33, s. 5193-5267
-
Forskningsöversikt (refereegranskat)abstract
- Ecosystems and the atmosphere: This review describes the state of understanding the processes involved in the exchange of trace gases and aerosols between the earth's surface and the atmosphere. The gases covered include NO, NO2, HONO, HNO3, NH3, SO2, DMS, Biogenic VOC, O-3, CH4, N2O and particles in the size range 1 nm-10 mu m including organic and inorganic chemical species. The main focus of the review is on the exchange between terrestrial ecosystems, both managed and natural and the atmosphere, although some new developments in ocean-atmosphere exchange are included. The material presented is biased towards the last decade, but includes earlier work, where more recent developments are limited or absent. New methodologies and instrumentation have enabled, if not driven technical advances in measurement. These developments have advanced the process understanding and upscaling of fluxes, especially for particles, VOC and NH3. Examples of these applications include mass spectrometric methods, such as Aerosol Mass Spectrometry (AMS) adapted for field measurement of atmosphere-surface fluxes using micrometeorological methods for chemically resolved aerosols. Also briefly described are some advances in theory and techniques in micrometeorology. For some of the compounds there have been paradigm shifts in approach and application of both techniques and assessment. These include flux measurements over marine surfaces and urban areas using micrometeorological methods and the up-scaling of flux measurements using aircraft and satellite remote sensing. The application of a flux-based approach in assessment of O-3 effects on vegetation at regional scales is an important policy linked development secured through improved quantification of fluxes. The coupling of monitoring, modelling and intensive flux measurement at a continental scale within the NitroEurope network represents a quantum development in the application of research teams to address the underpinning science of reactive nitrogen in the cycling between ecosystems and the atmosphere in Europe. Some important developments of the science have been applied to assist in addressing policy questions, which have been the main driver of the research agenda, while other developments in understanding have not been applied to their wider field especially in chemistry-transport models through deficiencies in obtaining appropriate data to enable application or inertia within the modelling community. The paper identifies applications, gaps and research questions that have remained intractable at least since 2000 within the specialized sections of the paper, and where possible these have been focussed on research questions for the coming decade.
|
|
| 32. |
|
|
| 33. |
|
|
| 34. |
|
|
| 35. |
- Jonsson, D., et al.
(författare)
-
Excited state polarizabilities in solution obtained by cubic response theory : Calculations on para-, ortho-, and meta-nitroaniline
- 1998
-
Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 109:15, s. 6351-6357
-
Tidskriftsartikel (refereegranskat)abstract
- We show that response theory implemented with a self-consistent reaction field theory model is a viable approach to simulate excited state polarizabilities of molecules in solution. The excited state polarizabilities are in this approach given by the double residue of the ground state cubic response functions, accounting for both equilibrium and nonequilibrium contributions to the interaction with the outer medium. The effects of the inertial polarization of the solvent on the polarizabilities of the solutes are shown to strongly depend on the solvent configuration, whether the solvent is in equilibrium or in nonequilibrium with the charge distribution of the investigated compound. The inertial polarization vector in the nonequilibrium solvent configuration represents the equilibrated solvent configuration when solvating the ground state of the solute. This inertial polarization vector is not in equilibrium with any of the excited states and therefore one observes a rather different behavior between nonequilibrium and equilibrium solvent descriptions of the solute. Illustrative calculations are presented for para-, meta-, and ortho-nitroanilines in gas and solution phases. Results have been compared with experimental data where available. © 1998 American Institute of Physics.
|
|
| 36. |
- Kawasaki, Jason K., et al.
(författare)
-
A simple electron counting model for half-Heusler surfaces
- 2018
-
Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 4
-
Tidskriftsartikel (refereegranskat)abstract
- Heusler compounds are a ripe platform for discovery and manipulation of emergent properties in topological and magnetic heterostructures. In these applications, the surfaces and interfaces are critical to performance; however, little is known about the atomic-scale structure of Heusler surfaces and interfaces or why they reconstruct. Using a combination of molecular beam epitaxy, core-level and angle-resolved photoemission, scanning tunneling microscopy, and density functional theory, we map the phase diagram and determine the atomic and electronic structures for several surface reconstructions of CoTiSb (001), a prototypical semiconducting half-Heusler. At low Sb coverage, the surface is characterized by Sb-Sb dimers and Ti vacancies, while, at high Sb coverage, an adlayer of Sb forms. The driving forces for reconstruction are charge neutrality and minimizing the number of Sb dangling bonds, which form metallic surface states within the bulk bandgap. We develop a simple electron counting model that explains the atomic and electronic structure, as benchmarked against experiments and first-principles calculations. We then apply the model to explain previous experimental observations at otherhalf-Heusler surfaces, including the topological semimetal PtLuSb and the half-metallic ferromagnet NiMnSb. The model provides a simple framework for understanding and predicting the surface structure and propertiesof these novel quantum materials.
|
|
| 37. |
- Kawasaki, Jason K., et al.
(författare)
-
Epitaxial growth and surface studies of the Half Heusler compound NiTiSn (001)
- 2013
-
Ingår i: Journal of Vacuum Science and Technology B. - : American Vacuum Society. - 1520-8567. ; 31:4
-
Tidskriftsartikel (refereegranskat)abstract
- The Half Heuslers are currently an attractive family of compounds for high temperature thermoelectrics research, and recently, there has been renewed interest since some of these compounds are proposed to be topological insulators. NiTiSn belongs to the family of 18 valence electron Half Heuslers that are predicted to be semiconducting, despite being composed entirely of metallic elements. The growth of the Half Heusler compound NiTiSn by molecular beam epitaxy is demonstrated. The NiTiSn films are epitaxial and single crystalline as observed by reflection high-energy electron diffraction and x-ray diffraction. Temperature dependent transport measurements suggest the films may be semiconducting, but with a high background carrier density indicative of a high density of electrically active defect states. Methods of protecting the sample surface for synchrotron-based photoemission measurements are explored. These methods may be applied to the study of surface electronic structure in unconventional materials. (C) 2013 American Vacuum Society.
|
|
| 38. |
|
|
| 39. |
- Lange, Lene, et al.
(författare)
-
Opportunities for Seaweed Biorefinery
- 2020. - 1
-
Ingår i: Sustainable Seaweed Technologies : Cultivation, Biorefinery and Application - Cultivation, Biorefinery and Application. - 9780128179444 - 9780128179437 ; , s. 3-31
-
Bokkapitel (refereegranskat)abstract
- This introductory chapter provides an overview of seaweed biorefinery opportunities, providing basis for multiple value chains, contributing to nutrition and health of a growing global population, to local job generation and development, to ecosystem services, and not the least to climate change mitigation and adaptation. A unique and rich diversity of the seaweed components provides the basis for the broad spectrum of value-chains described here. Red, brown, and green seaweeds are phylogenetically very different and this is reflected in their differences in growth, structure, and biochemical composition. Stable supply and high quality of feedstock are essential for unlocking the value-adding potential of seaweeds. A special focus of the chapter is to provide an overview of the range of different methods of seaweed production (through cultivation or from natural growth, collected or cut at the shore). Furthermore, the results of dedicated efforts to develop new deep-sea cultivation technologies of brown seaweed are highlighted. The chapter has a dual message with regard to seaweed processing: the need to develop more environmentally benign biological processing (to replace chemical processing); the advantage (regarding resource efficiency) and opportunities (social and economic) of designing seaweed biorefineries according to the cascading principle. Making optimized use of all valuable components of seaweed biomass, cascading from high-value products, such as skin care, health-promoting food and feed supplements and functional food ingredients; to lower-value products, such as plant stimulants, soil improvers, and bioenergy. Lastly, this introductory chapter provides global perspectives for future development of sustainable seaweed utilization, contributing to the UN-SDGs, providing livelihood and health for more.
|
|
| 40. |
- Liu, Yen-Po, et al.
(författare)
-
Hydrogen plasma enhanced oxide removal on GaSb planar and nanowire surfaces
- 2022
-
Ingår i: Applied Surface Science. - : Elsevier BV. - 0169-4332.
-
Tidskriftsartikel (refereegranskat)abstract
- Due to its high hole-mobility, GaSb is a highly promising candidate for high-speed p-channels in electronic devices. However, GaSb exhibits a comparably thick native oxide causing detrimental interface defects, which has been proven difficult to remove. Here we present full oxide removal from GaSb surfaces using effective hydrogen plasma cleaning, studied in-situ by synchrotron-based X-ray photoelectron spectroscopy under ultrahigh vacuum (UHV). GaSb nanowires turn out to be cleaned faster and more efficiently than planar substrates. Since the UHV conditions are not scalable for industrial sample processing, H-plasma cleaning is furthermore used as pre-treatment prior to atomic layer deposition (ALD) of a protective high-k layer to demonstrate the use of the cleaning step in a more realistic fabrication situation. We observe a cleaning effect of the H-plasma even in the ALD environment, but we also find residual Ga- and Sb-oxides at the GaSb-high-k interface, which we attribute to re-oxidation of the cleaned surface. Our results indicate that an improved control of the ALD reactor vacuum environment could realize oxide- and defect-free interfaces in GaSb-based electronics.
|
|
| 41. |
- Luo, Y., et al.
(författare)
-
Some recent developments of high-order response theory
- 1998
-
Ingår i: International Journal of Quantum Chemistry. - 0020-7608 .- 1097-461X. ; 70:1, s. 219-239
-
Tidskriftsartikel (refereegranskat)abstract
- We review some recent developments of high-order response theory and illustrate the utility of this theory for a selection of nonlinear properties. © 1998 John Willey & Sons, Inc.
|
|
| 42. |
- Mackey, Abigail L., et al.
(författare)
-
The influence of anti-inflammatory medication on exercise-induced myogenic precursor cell responses in humans
- 2007
-
Ingår i: Journal of applied physiology. - : American Physiological Society. - 8750-7587 .- 1522-1601. ; 103:2, s. 425-431
-
Tidskriftsartikel (refereegranskat)abstract
- The consumption of nonsteroidal anti-inflammatory drugs (NSAIDs) is widespread among athletes when faced with muscle soreness or injury, but the effects of NSAIDs on satellite cell activity in humans are unknown. To investigate this, 14 healthy male endurance athletes (mean peak oxygen consumption 62 ml x kg(-1) x min(-1)) volunteered for the study, which involved running 36 km. They were divided into two groups and received either 100 mg indomethacin per day or placebo. Muscle biopsies collected before the run and on days 1, 3, and 8 afterward were analyzed for satellite cells by immunohistochemistry with the aid of neural cell adhesion molecule (NCAM) and fetal antigen-1 (FA1) antibodies. Muscle biopsies were also collected from untrained individuals for comparison. Compared with preexercise levels, a 27% increase in the number of NCAM+ cells was observed on day 8 postexercise in the placebo group (P < 0.05), while levels remained similar at all time points in the NSAID group. No change was seen in the proportion of FA1+ cells, although lower levels were found in the muscle of endurance-trained athletes compared with untrained individuals (P < 0.05). These results suggest that ingestion of anti-inflammatory drugs attenuates the exercise-induced increase in satellite cell number, supporting the role of the cyclooxygenase pathway in satellite cell activity.
|
|
| 43. |
- Marçal, L. A.B., et al.
(författare)
-
Structural and chemical properties of anion exchanged CsPb(Br(1−x)Cl x )3 heterostructured perovskite nanowires imaged by nanofocused x-rays
- 2024
-
Ingår i: Nanotechnology. - 0957-4484. ; 35:26
-
Tidskriftsartikel (refereegranskat)abstract
- Over the last years metal halide perovskites have demonstrated remarkable potential for integration in light emitting devices. Heterostructures allow for tunable bandgap depending on the local anion composition, crucial for optoelectronic devices, but local structural effects of anion exchange in single crystals is not fully understood. Here, we investigate how the anion exchange of CsPbBr3 nanowires fully and locally exposed to HCl vapor affects the local crystal structure, using nanofocused x-rays. We study the nanoscale composition and crystal structure as function of HCl exposure time and demonstrate the correlation of anion exchange with changes in the lattice parameter. The local composition was measured by x-ray fluorescence and x-ray diffraction, with general agreement of both methods but with much less variation using latter. The heterostructured nanowires exhibit unintentional gradients in composition, both axially and radially. Ferroelastic domains are observed for all HCl exposure times, and the magnitude of the lattice tilt at the domain walls scales with the Cl concentration.
|
|
| 44. |
- Markljung, Ellen, et al.
(författare)
-
ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth
- 2009
-
Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 7:12, s. e1000256-
-
Tidskriftsartikel (refereegranskat)abstract
- A single nucleotide substitution in intron 3 of IGF2 in pigs abrogates a binding site for a repressor and leads to a 3-fold up-regulation of IGF2 in skeletal muscle. The mutation has major effects on muscle growth, size of the heart, and fat deposition. Here, we have identified the repressor and find that the protein, named ZBED6, is previously unknown, specific for placental mammals, and derived from an exapted DNA transposon. Silencing of Zbed6 in mouse C2C12 myoblasts affected Igf2 expression, cell proliferation, wound healing, and myotube formation. Chromatin immunoprecipitation (ChIP) sequencing using C2C12 cells identified about 2,500 ZBED6 binding sites in the genome, and the deduced consensus motif gave a perfect match with the established binding site in Igf2. Genes associated with ZBED6 binding sites showed a highly significant enrichment for certain Gene Ontology classifications, including development and transcriptional regulation. The phenotypic effects in mutant pigs and ZBED6-silenced C2C12 myoblasts, the extreme sequence conservation, its nucleolar localization, the broad tissue distribution, and the many target genes with essential biological functions suggest that ZBED6 is an important transcription factor in placental mammals, affecting development, cell proliferation, and growth.
|
|
| 45. |
- Mikkelsen, L. H., et al.
(författare)
-
Genomic and immunohistochemical characterisation of a lacrimal gland oncocytoma and review of literature
- 2017
-
Ingår i: Oncology Letters. - : Spandidos Publications. - 1792-1074 .- 1792-1082. ; 14:4, s. 4176-4182
-
Tidskriftsartikel (refereegranskat)abstract
- The aim of the present study was to report the genetic and immunohistochemical profile of a rare case of lacrimal gland oncocytoma. A 20-year-old male underwent magnetic resonance imaging (MRI) due to viral encephalitis. Notably, the MRI revealed a multicystic tumor in the left lacrimal gland. A lateral orbitotomy was performed and the tumor was completely excised. Four months following surgery, the patient was free of symptoms. Histopathologically, the tumor was composed of large, eosinophilic and polyhedral cells with small round nuclei. The tumor cells stained strongly for antimitochondrial antibody MU213-UC, cytokeratin (CK) 5/6, CK 7, CK 17, CK 8/18 and CK 19. The final diagnosis was an oncocytoma of the lacrimal gland without any signs of malignancy. Array-based comparative genomic hybridisation demonstrated a gain of one copy of chromosome 8 and loss of one copy of chromosome 22 as the sole genomic imbalances. These chromosomal alterations have not previously been identified in oncocytoma and may be specific to lacrimal gland oncocytoma. Sequencing of the mitochondrial genome demonstrated multiple alterations of the NADH-ubiquinone oxidoreductase chain 5 (ND5) gene involved in mitochondrial oxidative phosphorylation. This may support the notion of a common genetic background of oncocytic lesions in the lacrimal gland and other anatomical sites. © 2017, Spandidos Publications. All rights reserved.
|
|
| 46. |
- Mikkelä, M.-H., et al.
(författare)
-
Bismuth-oxide nanoparticles : study in a beam and as deposited
- 2024
-
Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 26:13, s. 10369-10381
-
Tidskriftsartikel (refereegranskat)abstract
- Bi2O3 is a promising material for solid-oxide fuel cells (SOFC) due to the high ionic conductivity of some phases. The largest value is reached for its δ-phase, but it is normally stable at temperatures too high for SOFC operation, while nanostructured oxide is believed to have more suitable stabilization temperature. However, to manufacture such a material with a controlled chemical composition is a challenging task. In this work, we investigated the fabrication of nanostructured Bi2O3 films formed by deposition of free Bi-oxide nanoparticles created in situ. The particle-production method was based on reactive sputtering and vapour aggregation. Depending on the fabrication conditions, the nanoparticles contained either a combination of Bi–metal and Bi-oxide, or only Bi-oxide. Prior to deposition, the free particles were probed in the beam – by synchrotron-based photoelectron spectroscopy (PES), which allowed assessing their composition "on the-fly". The nanoparticle films obtained after deposition were studied by PES, scanning electron microscopy, transmission electron microscopy, and electron diffraction. The films' chemical composition, grain dimensions, and crystal structure were probed. Our analysis suggests that our method produced Bi-oxide films in more than one polymorph of Bi2O3.
|
|
| 47. |
|
|
| 48. |
- Norman, P., et al.
(författare)
-
Hyperpolarizability depolarization ratios of nitroanilines
- 1997
-
Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 107:21, s. 9063-9066
-
Tidskriftsartikel (refereegranskat)abstract
- The depolarization ratios for the first hyperpolarizabilities of para-, meta-, and ortho-nitroanilines have been calculated in gas and solution phases. The results resolve ambiguities in the interpretation of experimental results for these quantities, and pinpoint the actual problems in previous simulations. It is argued that extraction of individual components of β of low symmetry molecules from experimental depolarization measurements alone is difficult, and that the support from simulations to extract the proper information is indispensable in most cases.
|
|
| 49. |
- Olsen, Jogvan Magnus Haugaard, et al.
(författare)
-
Dalton Project : A Python platform for molecular- and electronic-structure simulations of complex systems
- 2020
-
Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 152:21
-
Tidskriftsartikel (refereegranskat)abstract
- The Dalton Project provides a uniform platform access to the underlying full-fledged quantum chemistry codes Dalton and LSDalton as well as the PyFraME package for automatized fragmentation and parameterization of complex molecular environments. The platform is written in Python and defines a means for library communication and interaction. Intermediate data such as integrals are exposed to the platform and made accessible to the user in the form of NumPy arrays, and the resulting data are extracted, analyzed, and visualized. Complex computational protocols that may, for instance, arise due to a need for environment fragmentation and configuration-space sampling of biochemical systems are readily assisted by the platform. The platform is designed to host additional software libraries and will serve as a hub for future modular software development efforts in the distributed Dalton community.
|
|
| 50. |
- Patel, Sahil J., et al.
(författare)
-
Surface and electronic structure of epitaxial PtLuSb (001) thin films
- 2014
-
Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 104:20
-
Tidskriftsartikel (refereegranskat)abstract
- The surface and electronic structure of single crystal thin films of PtLuSb (001) grown by molecular beam epitaxy were studied. Scanning tunneling spectroscopy (STS), photoemission spectroscopy, and temperature dependent Hall measurements of PtLuSb thin films are consistent with a zero-gap semiconductor or semi-metal. STS and photoemission measurements show a decrease in density of states approaching the Fermi level for both valence and conduction bands as well as a slight shift of the Fermi level position into the valence band. Temperature dependent Hall measurements also corroborate the Fermi level position by measurement of p-type carriers. (C) 2014 AIP Publishing LLC.
|
|
