| 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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| 4. |
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| 5. |
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| 6. |
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| 7. |
- 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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| 8. |
- Sadlej, J., et al.
(författare)
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Properties and Spectroscopies
- 2007
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Ingår i: Continuum Solvation Models in Chemical Physics: From Theory to Applications. - Chichester, UK : John Wiley & Sons. - 9780470029381 ; , s. 125-312
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Bokkapitel (refereegranskat)
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| 9. |
- 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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| 10. |
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| 11. |
- Jonsson, D., et al.
(författare)
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Excited state polarizabilities in solution obtained by cubic response theory : Calculations on para-, ortho-, and meta-nitroaniline
- 1998
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 109:15, s. 6351-6357
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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.
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| 12. |
- Luo, Y., et al.
(författare)
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Dielectric and optical properties of pure liquids by means of ab initio reaction field theory
- 1998
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Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - : American Physical Society (APS). - 1063-651X .- 1095-3787. ; 57:4, s. 4778-4785
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Tidskriftsartikel (refereegranskat)abstract
- A general Onsager-type reaction field theory approach for simulating dielectric and optical properties is proposed, thereby giving a unified description for both macroscopic and microscopic properties of pure liquids. A demonstration is given for ab initio computations of the refractive index, the density fluctuation of the refractive index, and the local field factors of benzene and acetonitrile in the liquid phase, showing good agreement with available experimental data.
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| 13. |
- Luo, Y., et al.
(författare)
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Some recent developments of high-order response theory
- 1998
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Ingår i: International Journal of Quantum Chemistry. - 0020-7608 .- 1097-461X. ; 70:1, s. 219-239
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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.
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| 14. |
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| 15. |
- Norman, P., et al.
(författare)
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Hyperpolarizability depolarization ratios of nitroanilines
- 1997
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 107:21, s. 9063-9066
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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.
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| 16. |
- Stelzenmuller, V., et al.
(författare)
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Evaluation of marine spatial planning requires fit for purpose monitoring strategies
- 2021
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Ingår i: Journal of Environmental Management. - : Elsevier BV. - 0301-4797. ; 278
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Tidskriftsartikel (refereegranskat)abstract
- Marine spatial planning (MSP) has rapidly become the most widely used integrated, place-based management approach in the marine environment. Monitoring and evaluation of MSP is key to inform best practices, adaptive management and plan iteration. While standardised evaluation frameworks cannot be readily applied, accounting for evaluation essentials such as the definition of evaluation objectives, indicators and stakeholder engagement of stakeholders is a prerequisite for meaningful evaluation outcomes. By way of a literature review and eleven practical MSP case studies, we analysed present day trends in evaluation approaches and unravelled the adoption of evaluation essentials for three categories for monitoring and evaluation for plan making, plan outcomes, and policy implementation. We found that at a global scale the focus of MSP evaluation has shifted over the past decade from evaluating predominantly plan outcomes towards the evaluation of plan making. Independent of the scope of the evaluation, evaluation approaches varied greatly from formal and structured processes, building for instance on MSP goals and objectives, to informal processes based on stakeholder interviews. We noted a trend in the adoption of formalised approaches where MSP evaluations have increasingly become linked to MSP policy goals and objectives. However, the enhanced use of MSP objectives and indicators did not result in a more straightforward reporting of outcomes, e.g. such as the achievement of specific MSP objectives. Overall, we found weak linkages between defined MSP objectives, indicators and available monitoring data. While the apparent shift towards a focus on objectives is promising, we highlight the need of fit-for purpose monitoring data to enable effective evaluation of those objectives. Hence, effective MSP and adaptive management processes require customised and concurrent monitoring and evaluation strategies and procedures. We argue that evaluation processes would also benefit from a better understanding of the general environmental, socio-economic and socio-cultural effects of MSP. Therefore, to understand better environmental effects of MSP, we praise that forthcoming MSP processes need to deepen the understanding and considerations of cause-effect pathways between human activities and changes of ecosystem state through the adoption of targeted cumulative effects assessments.
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| 17. |
- Sylvester-Hvid, K. O., et al.
(författare)
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Cubic optical response of molecules in a nonequilibrium and equilibrium solvation model
- 1999
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 103:42, s. 8375-8383
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Tidskriftsartikel (refereegranskat)abstract
- The cubic response equations governing nonequilibrium and equilibrium solvation in the continuum approach are derived and implemented. We consider solvent effects on the frequency dependent second hyperpolarizability. We illustrate the effects of optical and static dielectric constants through sample calculations on H2O and H2CO.
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| 18. |
- Sylvester-Hvid, K. O., et al.
(författare)
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Nonlinear optical response of molecules in a nonequilibrium solvation model
- 1998
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 109:13, s. 5576-5584
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Tidskriftsartikel (refereegranskat)abstract
- The response equations governing nonequilibrium solvation in the continuum approach are derived and implemented for second order in response theory. Applications to a simple benchmark system consisting of a solvated water molecule are presented. We consider the role of nonequilibrium solvent configurations on the first hyperpolarizability. Effects of solvation parameters, such as optical and static dielectric constants, and frequency dispersion are discussed.
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| 19. |
- Sylvester-Hvid, K. O., et al.
(författare)
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Sign change of hyperpolarizabilities of solvated water, revised : Effects of equilibrium and nonequilibrium solvation
- 2004
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 108:41, s. 8961-8965
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Tidskriftsartikel (refereegranskat)abstract
- The second harmonic and electro-optical responses for the water molecule in its liquid state are theoretically revised. The continuum, semicontinuum, and supermolecular solvation models are employed using quadratic response theory at the Hartree-Fock level, either in the equilibrium or nonequilibrium implementation. The experimentally observed sign change of the second harmonic response of water on liquefaction is reproduced using the supermolecular and semicontinuum model for both equilibrium and nonequilibrium solvation. The conclusions of a previous study, which rested upon linear response theory in an equilibrium implementation, are confirmed. Also, the assumption of Kleinman symmetry and dispersion is addressed.
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| 20. |
- Aidas, Kestutis, et al.
(författare)
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On the performance of quantum chemical methods to predict solvatochromic effects: The case of acrolein in aqueous solution.
- 2008
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 128:19, s. 1-194503
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Tidskriftsartikel (refereegranskat)abstract
- The performance of the Hartree-Fock method and the three density functionals B3LYP, PBE0, and CAM-B3LYP is compared to results based on the coupled cluster singles and doubles model in predictions of the solvatochromic effects on the vertical n-->pi(*) and pi-->pi(*) electronic excitation energies of acrolein. All electronic structure methods employed the same solvent model, which is based on the combined quantum mechanics/molecular mechanics approach together with a dynamical averaging scheme. In addition to the predicted solvatochromic effects, we have also performed spectroscopic UV measurements of acrolein in vapor phase and aqueous solution. The gas-to-aqueous solution shift of the n-->pi(*) excitation energy is well reproduced by using all density functional methods considered. However, the B3LYP and PBE0 functionals completely fail to describe the pi-->pi(*) electronic transition in solution, whereas the recent CAM-B3LYP functional performs well also in this case. The pi-->pi(*) excitation energy of acrolein in water solution is found to be very dependent on intermolecular induction and nonelectrostatic interactions. The computed excitation energies of acrolein in vacuum and solution compare well to experimental data.
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| 21. |
- Alexopoulou, E., et al.
(författare)
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Embryo Morphokinetics and Blastocyst Development After GnRH Agonist versus hCG Triggering in Normo-ovulatory Women: a Secondary Analysis of a Multicenter Randomized Controlled Trial
- 2021
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Ingår i: Reproductive Sciences. - : Springer Science and Business Media LLC. - 1933-7191 .- 1933-7205. ; 28, s. 2972-2981
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Tidskriftsartikel (refereegranskat)abstract
- Gonadotropin-releasing hormone agonist (GnRHa) for final oocyte maturation, along with vitrification of all usable embryos followed by transfer in a subsequent frozen-thawed cycle, is the most effective strategy to avoid ovarian hyperstimulation syndrome (OHSS). However, less is known about the ovulation induction triggers effect on early embryo development and blastocyst formation. This study is a secondary analysis of a multicenter, randomized controlled trial, with the aim to compare embryo development in normo-ovulatory women, randomized to GnRHa or human chorionic gonadotropin (hCG) trigger. In all, 4056 retrieved oocytes were observed, 1998 from the GnRHa group (216 women) and 2058 from the hCG group (218 women). A number of retrieved oocytes, mature and fertilized oocytes, and high-quality embryos and blastocysts were similar between the groups. A sub-analysis in 250 women enrolled at the main trial site including 2073 oocytes was conducted to compare embryo morphokinetics and cleavage patterns with EmbryoScope time-lapse system. In total, 1013 oocytes were retrieved from the GnRHa group (124 women) and 1060 oocytes were retrieved from the hCG group (126 women). Morphokinetic parameters and cleavage patterns were comparable between the groups. However, embryos derived from the GnRHa group were less likely to perform rolling during their development than the embryos from the hCG trigger group (OR = 0.41 (95%CI 0.25; 0.67), p-value 0.0003). The comparable results on embryo development and utilization rates between the GnRHa and hCG triggers is of clinical relevance to professionals and infertile patients, when GnRHa trigger and freeze-all is performed to avoid OHSS development. ClinicalTrials.gov Identifier: NCT02746562
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| 22. |
- Elm, J., et al.
(författare)
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Rayleigh light scattering properties of atmospheric molecular clusters consisting of sulfuric acid and bases
- 2015
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 17:24, s. 15701-15709
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Tidskriftsartikel (refereegranskat)abstract
- The Rayleigh light scattering properties of (H2SO4)a(NH3)b and (H2SO4)a((CH3)2NH)b atmospheric molecular clusters have been investigated using a response theory approach. Using density functional theory the molecular structures and stepwise formation free energies of clusters with a and b up to 4 have been re-investigated. The Rayleigh scattering intensities are calculated from the dipole polarizability tensor α using the CAM-B3LYP functional by applying linear response methods. The intrinsic scattering properties of (H2SO4)a(NH3)b and (H2SO4)a((CH3)2NH)b indicate that amine containing clusters scatter light significantly more efficiently then their ammonia containing counterparts. Using the Atmospheric Cluster Dynamics Code (ACDC) the steady state cluster concentrations are estimated and the effective scattering is calculated. The effective scattering is shown to be highly dependent on the estimated concentrations and indicates that there exist competitive pathways, such as nucleation and coagulation, which influence the cluster distributions. The frequency dependence of the scattering is found to depend on the cluster composition and show increased responses when clusters contain more bases than acid molecules. Based on structures obtained using semi-empirical molecular dynamics simulations the Rayleigh scattering properties of clusters with up to 20 acid-base pairs are evaluated. This study represents the first step towards gaining a fundamental understanding of the scattering properties of small atmospheric clusters in the ambient atmosphere.
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| 23. |
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| 24. |
- 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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| 25. |
- Hillers-Bendtsen, A. E., et al.
(författare)
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Modeling Absorption and Emission Spectroscopies of Symmetric and Asymmetric Azaoxahelicenes in Vacuum and Solution
- 2022
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 126:37, s. 6467-6472
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Tidskriftsartikel (refereegranskat)abstract
- Helicenes are of general interest due to the significant chiral signals in both absorption- and emission-based spectroscopy. Herein, the spectroscopic properties of four recently synthesized azaoxahelicenes are studied using density functional theory methods. The azaoxahelicenes have 7, 9, 10, and 13 units and one to two complete turns of the structure. UV-vis absorption and electronic circular dichroism spectra are determined both in vacuum and in solution using explicit solvation through a combined molecular dynamics/polarizable embedding framework. Additionally, emission and circularly polarized luminescence spectra are determined based on vibronic calculations. The resulting spectra are in good agreement with the experimentally available data, highlighting that both absorption- and emission-based spectra of the systems can be modeled computationally such that reliable predictions can be made for systems that are yet to be synthesized.
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| 26. |
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| 27. |
- Kongsted, Jacob, et al.
(författare)
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Coupled cluster calculations of the optical rotation of S-propylene oxide in gas phase and solution
- 2005
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Ingår i: Chemical Physics Letters. - : Elsevier BV. - 0009-2614. ; 401:4-6, s. 385-392
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Tidskriftsartikel (refereegranskat)abstract
- We present ab initio calculations of the optical rotation of S-propylene oxide in both gas phase and solution using the coupled cluster methodology combined with a dielectric continuum description of the solvent. The coupled cluster calculations are performed using the CCS, CC2, CCSD and CC3 methods. None of the presented gas phase results are in accord with the experimental sign of the optical rotation at 355 nm. Thereby, the experimental sign change between the gas phase and the cyclohexane,solution optical rotation at 355 nm is not reproduced theoretically. The vibrational effects are considered to be significant and may be of crucial importance in order to bring accordance between the calculated and the experimentally established sign of the gas phase optical rotation at 355 nm. (C) 2004 Elsevier B.V. All rights reserved.
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| 28. |
- Lin, Yan-Shih, et al.
(författare)
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Optimal stomatal behaviour around the world
- 2015
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Ingår i: Nature Climate Change. - : Springer Science and Business Media LLC. - 1758-678X .- 1758-6798. ; 5, s. 459-464
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Tidskriftsartikel (refereegranskat)abstract
- Stomatal conductance (gs) is a key land-surface attribute as it links transpiration, the dominant component of global land evapotranspiration, and photosynthesis, the driving force of the global carbon cycle. Despite the pivotal role of gs in predictions of global water and carbon cycle changes, a globalscale database and an associated globally applicable model of gs that allow predictions of stomatal behaviour are lacking. Here,we present a database of globally distributed gs obtained in the field for a wide range of plant functional types (PFTs) and biomes. We find that stomatal behaviour differs among PFTs according to their marginal carbon cost of water use, as predicted by the theory underpinning the optimal stomatal model1 and the leaf and wood economics spectrum2,3.We also demonstrate a global relationship with climate. These findings provide a robust theoretical framework for understanding and predicting the behaviour of gs across biomes and across PFTs that can be applied to regional, continental and global-scale modelling of ecosystem productivity, energy balance and ecohydrological processes in a future changing climate.
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| 29. |
- Lin, Yan-Shih, et al.
(författare)
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Optimal stomatal behaviour around the world
- 2015
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Ingår i: Nature Climate Change. - 1758-6798 .- 1758-678X. ; 5:5, s. 459-464
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Tidskriftsartikel (refereegranskat)abstract
- Stomatal conductance (g(s)) is a key land-surface attribute as it links transpiration, the dominant component of global land evapotranspiration, and photosynthesis, the driving force of the global carbon cycle. Despite the pivotal role of g(s) in predictions of global water and carbon cycle changes, a global-scale database and an associated globally applicable model of g(s) that allow predictions of stomatal behaviour are lacking. Here, we present a database of globally distributed g(s) obtained in the field for a wide range of plant functional types (PFTs) and biomes. We find that stomatal behaviour differs among PFTs according to their marginal carbon cost of water use, as predicted by the theory underpinning the optimal stomatal model(1) and the leaf and wood economics spectrum(2,3). We also demonstrate a global relationship with climate. These findin g(s) provide a robust theoretical framework for understanding and predicting the behaviour of g(s) across biomes and across PFTs that can be applied to regional, continental and global-scale modelling of ecosystem productivity, energy balance and ecohydrological processes in a future changing climate.
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| 30. |
- Murugan, N Arul, et al.
(författare)
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Hybrid density functional theory/molecular mechanics calculations of two-photon absorption of dimethylamino nitro stilbene in solution
- 2011
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 13:27, s. 12506-12516
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Tidskriftsartikel (refereegranskat)abstract
- The dimethylamino nitro stilbene (DANS) molecule is studied for exploring solvent effects on two-photon absorption using the quantum mechanical/molecular mechanical (QM/MM) response theory approach, where the quantum part is represented by density functional theory. We have explored the role of geometrical change of the chromophore in solution, the importance of taking a dynamical average over the sampled structures and the role of a granular representation of the polarization and electrostatic interactions with the classically described medium. The line shape function was simulated by the QM/MM technique thereby allowing for non-empirical prediction of the absolute two-photon cross section. We report a maximum in the TPA cross section for a medium of intermediate solvent polarity (i.e. in chloroform) and provide the grounds for an explanation of this effect which recently has been experimentally observed for a series of charge transfer species in solvents of different polarity. The calculations of absorption energies reproduce well the positive solvatochromic behavior of DANS and are in good agreement with experimental spectra available for the chloroform and DMSO solvents. In line with recent development of the QM/MM response technique for color modeling, we find this methodology to offer a versatile tool to predict and analyze two-photon absorption phenomena taking place within a medium.
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| 31. |
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| 32. |
- Sjöqvist, Jonas, et al.
(författare)
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QM/MM-MD simulations of conjugated polyelectrolytes : A study of luminescent conjugated oligothiophenes for use as biophysical probes
- 2014
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 118:19, s. 3419-3428
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Tidskriftsartikel (refereegranskat)abstract
- A methodological development is reported for the study of luminescence properties of conjugated polyelectrolytes, encompassing systems in which dihedral rotational barriers are easily overcome at room temperature. The components of the model include (i) a molecular mechanics (MM) force field description of the solvent in its electronic ground state as well as the chromophore in its electronic ground and excited states, (ii) a conformational sampling by means of classical molecular dynamics (MD) in the respective electronic states, and (iii) spectral response calculations by means of the quantum mechanics/molecular mechanics QM/MM approach. A detailed analysis of the combined polarization effects of the ionic moiety and the polar water solvent is presented. At an increased computational cost of 30% compared to a calculation excluding the solvent, the error in the transition wavelength of the dominant absorption band is kept as small as 1 nm as compared to the high-quality benchmark result, based largely on a QM description of the solvent. At a reduced computational cost the error of the same quantity is kept as small as 6 nm, with the cost reduction being the result of an effective description of the effects of the solvent by means of replacing the carboxylate ions with neutral hydrogens. In absorption spectroscopy, the obtained best theoretical results are in excellent agreement with the experimental benchmark measurement, regarding excitation energies as well as band intensities and profiles. In fluorescence spectroscopy, the experimental spectrum shows a vibrational progression that is not addressed by theory, but the theoretical band position is in excellent agreement with experiment, with a highly accurate description of the Stokes shift as a result.
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| 33. |
- Stenman, Göran, 1953, et al.
(författare)
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Chromosome Translocations, Gene Fusions, and Their Molecular Consequences in Pleomorphic Salivary Gland Adenomas
- 2022
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Ingår i: Biomedicines. - : MDPI AG. - 2227-9059. ; 10:8
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Tidskriftsartikel (refereegranskat)abstract
- Salivary gland tumors are a heterogeneous group of tumors originating from the major and minor salivary glands. The pleomorphic adenoma (PA), which is the most common subtype, is a benign lesion showing a remarkable morphologic diversity and that, upon recurrence or malignant transformation, can cause significant clinical problems. Cytogenetic studies of >500 PAs have revealed a complex and recurrent pattern of chromosome rearrangements. In this review, we discuss the specificity and frequency of these rearrangements and their molecular/clinical consequences. The genomic hallmark of PA is translocations with breakpoints in 8q12 and 12q13-15 resulting in gene fusions involving the transcription factor genes PLAG1 and HMGA2. Until recently, the association between these two oncogenic drivers was obscure. Studies of the Silver-Russel syndrome, a growth retardation condition infrequently caused by mutations in IGF2/HMGA2/PLAG1, have provided new clues to the understanding of the molecular pathogenesis of PA. These studies have demonstrated that HMGA2 is an upstream regulator of PLAG1 and that HMGA2 regulates the expression of IGF2 via PLAG1. This provides a novel explanation for the 8q12/12q13-15 aberrations in PA and identifies IGF2 as a major oncogenic driver and therapeutic target in PA. These studies have important diagnostic and therapeutic implications for patients with PA.
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| 34. |
- Stormlund, S., et al.
(författare)
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Freeze-all versus fresh blastocyst transfer strategy during in vitro fertilisation in women with regular menstrual cycles: multicentre randomised controlled trial
- 2020
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Ingår i: Bmj-British Medical Journal. - : BMJ. - 1756-1833. ; 370
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE To compare the ongoing pregnancy rate between a freeze-all strategy and a fresh transfer strategy in assisted reproductive technology treatment. DESIGN Multicentre, randomised controlled superiority trial. SETTING Outpatient fertility clinics at eight public hospitals in Denmark, Sweden, and Spain. PARTICIPANTS 460 women aged 18-39 years with regular menstrual cycles starting their first, second, or third treatment cycle of in vitro fertilisation or intracytoplasmic sperm injection. INTERVENTIONS Women were randomised at baseline on cycle day 2 or 3 to one of two treatment groups: the freeze-all group (elective freezing of all embryos) who received gonadotropin releasing hormone agonist triggering and single frozen-thawed blastocyst transfer in a subsequent modified natural cycle; or the fresh transfer group who received human chorionic gonadotropin triggering and single blastocyst transfer in the fresh cycle. Women in the fresh transfer group with more than 18 follicles larger than 11 mm on the day of triggering had elective freezing of all embryos and postponement of transfer as a safety measure. MAIN OUTCOME MEASURES The primary outcome was the ongoing pregnancy rate defined as a detectable fetal heart beat after eight weeks of gestation. Secondary outcomes were live birth rate, positive human chorionic gonadotropin rate, time to pregnancy, and pregnancy related, obstetric, and neonatal complications. The primary analysis was performed according to the intention-to-treat principle. RESULTS Ongoing pregnancy rate did not differ significantly between the freeze-all and fresh transfer groups (27.8% (62/223) v 29.6% (68/230); risk ratio 0.98, 95% confidence interval 0.87 to 1.10, P=0.76). Additionally, no significant difference was found in the live birth rate (27.4% (61/223) for the freeze-all group and 28.7% (66/230) for the fresh transfer group; risk ratio 0.98, 95% confidence interval 0.87 to 1.10, P=0.83). No significant differences between groups were observed for positive human chorionic gonadotropin rate or pregnancy loss, and none of the women had severe ovarian hyperstimulation syndrome; only one hospital admission related to this condition occurred in the fresh transfer group. The risks of pregnancy related, obstetric, and neonatal complications did not differ between the two groups except for a higher mean birth weight after frozen blastocyst transfer and an increased risk of prematurity after fresh blastocyst transfer. Time to pregnancy was longer in the freeze-all group. CONCLUSIONS In women with regular menstrual cycles, a freeze-all strategy with gonadotropin releasing hormone agonist triggering for final oocyte maturation did not result in higher ongoing pregnancy and live birth rates than a fresh transfer strategy. The findings warrant caution in the indiscriminate application of a freeze-all strategy when no apparent risk of ovarian hyperstimulation syndrome is present.
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| 35. |
- Sun, J, et al.
(författare)
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Structural determination of a low-symmetry surface by low-energy electron diffraction and ab initio calculations: Bi(110)
- 2006
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. ; 74
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Tidskriftsartikel (refereegranskat)abstract
- he surface structure of Bi(110) has been investigated by low-energy electron diffraction (LEED) intensity analysis and by first-principles calculations. Diffraction patterns at a sample temperature of 110 K and normal incidence reveal a bulk truncated (1×1) surface without indication of any structural reconstruction despite the presence of dangling bonds on the surface layer. Good agreement is obtained between the calculated and measured diffraction intensities for this complex, low-symmetry surface containing only one mirror-plane symmetry element. No significant interlayer spacing relaxations are found. The Debye temperature for the surface layer is found to be lower than in the bulk, which is indicative of larger vibrational atomic amplitudes at the surface. Meanwhile, the second layer shows a Debye temperature close to the bulk value. The experimental results for the relaxations agree well with those of our first-principles calculation.
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| 36. |
- Todorova, M, et al.
(författare)
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The Pd(100)-(root 5 x root 5)R27 degrees-O surface oxide revisited
- 2003
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Ingår i: Surface Science. - 0039-6028. ; 541:1-3, s. 101-112
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Tidskriftsartikel (refereegranskat)abstract
- Combining high-resolution core-level spectroscopy, scanning tunneling microscopy and density-functional theory calculations we reanalyze the Pd(100)-(root5 x root5)R27degrees-O surface oxide phase. We find that the prevalent structural model, a rumpled PdO(001) film suggested by previous low energy electron diffraction (LEED) work [Surf. Sci. 494 (2001) L799], is incompatible with all three employed methods. Instead, we suggest the two-dimensional film to consist of a strained PdO(101) layer on top of Pd(100). LEED intensity calculations show that this model is compatible with the experimental data of Saidy et al. (C) 2003 Elsevier B.V. All rights reserved.
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| 37. |
- Warthegau, Stefan S., et al.
(författare)
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Heterocyclic [9]Helicenes Exhibiting Bright Circularly Polarized Luminescence
- 2023
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Ingår i: Chemistry - A European Journal. - : Wiley. - 0947-6539 .- 1521-3765. ; 29:58
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Tidskriftsartikel (refereegranskat)abstract
- We describe a concise synthetic strategy for the preparation of heterocyclic [9]helicenes and a simple preparative-scale protocol for the optical resolution of the resulting M- and P-enantiomers. The helicenes were characterized by single-crystal X-ray diffraction along with a range of spectroscopic and computational techniques. A fluorescence quantum yield of up to 65 % was observed, and the chiroptical properties of both M- and P-helicenes revealed large dissymmetry factors. The circularly polarized luminescence brightness reaches up to 17 M−1 cm−1, as measured experimentally and verified computationally, which makes this the highest circularly polarized luminescence brightness among heterocyclic helicenes. We describe how chiroptical properties (both circular dichroism and circularly polarized luminescence) can be described and predicted using quantum chemical calculations. The synthetic approach also reveals by-products that originate from internal oxidation reactions, presumably mediated by the close proximity of the π-surfaces in the helicene structure.
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