| 1. |
- Niemi, MEK, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 2. |
- Kanai, M, et al.
(författare)
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- 2023
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swepub:Mat__t
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| 3. |
- 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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| 4. |
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| 5. |
- Hagara, Jakub, et al.
(författare)
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Novel highly substituted thiophene-based n-type organic semiconductor : structural study, optical anisotropy and molecular control
- 2020
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Ingår i: CrystEngComm. - : Royal Society of Chemistry. - 1466-8033 .- 1466-8033. ; 22:42, s. 7095-7103
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Tidskriftsartikel (refereegranskat)abstract
- Oligothiophenes and their functionalized derivatives have been shown to be a viable option for high-performance organic electronic devices. The functionalization of oligothiophene-based materials allows further tailoring of their properties for specific applications. We have synthesized a new thiophene-based molecule 1-[5'-(2-naphthyl)-2,2'-bithiophen-5-yl]hexan-1-one (NCOH), and we have studied the optical and structural properties of NCOH thin films. NCOH is a highly substituted member of the oligothiophene family, designed to improve its molecular stacking, where the presence of an electron-withdrawing group enhances its electron transport capabilities. Employing in situ and time-resolved grazing-incidence wide-angle X-ray scattering (GIWAXS) measurements, we determined the NCOH thin film crystallographic structure and its evolution starting from the early stages of the film growth. We observed strong optical anisotropy resulting from a highly oriented crystallographic structure. Additionally, we investigated the substrate-induced changes of the molecular orientation utilizing the few-layer MoS2 with different orientations of the atomic layers. This study, with its primary focus on the fundamentally important n-type molecular semiconductor, contributes to the field of organic-based (opto-)electronics.
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| 6. |
- Huber, Dominik, et al.
(författare)
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PFASST with dynamic resource management for large-scale applications
- 2023
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Dynamic resource management is a fairly recent development made to improve the flexibility of job scheduling. MPI-based approach [1] makes this possible by treating resources on a set granularity and performs set operations whenever changes are made. Due to the extreme resource requirements, using dynamic resources will likely be compulsory for parallel-in-time methods. Development towards this has been made by prototyping an interface for dynamic resource management and then incorporating it into LibPFASST to provide proof of concept. The intent of this poster is to motivate further investigation and exploration of dynamic resources for large-scale applications such as weather/climate simulations, molecular dynamics, graph design and more.
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| 7. |
- Beck, Christian, et al.
(författare)
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Short-Time Transport Properties of Bidisperse Suspensions of Immunoglobulins and Serum Albumins Consistent with a Colloid Physics Picture.
- 2022
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 126:38, s. 7400-7408
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Tidskriftsartikel (refereegranskat)abstract
- The crowded environment of biological systems such as the interior of living cells is occupied by macromolecules with a broad size distribution. This situation of polydispersity might influence the dependence of the diffusive dynamics of a given tracer macromolecule in a monodisperse solution on its hydrodynamic size and on the volume fraction. The resulting size dependence of diffusive transport crucially influences the function of a living cell. Here, we investigate a simplified model system consisting of two constituents in aqueous solution, namely, of the proteins bovine serum albumin (BSA) and bovine polyclonal gamma-globulin (Ig), systematically depending on the total volume fraction and ratio of these constituents. From high-resolution quasi-elastic neutron spectroscopy, the separate apparent short-time diffusion coefficients for BSA and Ig in the mixture are extracted, which show substantial deviations from the diffusion coefficients measured in monodisperse solutions at the same total volume fraction. These deviations can be modeled quantitatively using results from the short-time rotational and translational diffusion in a two-component hard sphere system with two distinct, effective hydrodynamic radii. Thus, we find that a simple colloid picture well describes short-time diffusion in binary mixtures as a function of the mixing ratio and the total volume fraction. Notably, the self-diffusion of the smaller protein BSA in the mixture is faster than the diffusion in a pure BSA solution, whereas the self-diffusion of Ig in the mixture is slower than in the pure Ig solution.
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| 8. |
- Hirschmann, Frank, et al.
(författare)
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Effects of flexibility in coarse-grained models for bovine serum albumin and immunoglobulin G
- 2023
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Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 158:8
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Tidskriftsartikel (refereegranskat)abstract
- We construct a coarse-grained, structure-based, low-resolution, 6-bead flexible model of bovine serum albumin (BSA, PDB: 4F5S), which is a popular example of a globular protein in biophysical research. The model is obtained via direct Boltzmann inversion using all-atom simulations of a single molecule, and its particular form is selected from a large pool of 6-bead coarse-grained models using two suitable metrics that quantify the agreement in the distribution of collective coordinates between all-atom and coarse-grained Brownian dynamics simulations of solutions in the dilute limit. For immunoglobulin G (IgG), a similar structure-based 12-bead model has been introduced in the literature [Chaudhri et al., J. Phys. Chem. B 116, 8045 (2012)] and is employed here to compare findings for the compact BSA molecule and the more anisotropic IgG molecule. We define several modified coarse-grained models of BSA and IgG, which differ in their internal constraints and thus account for a variation of flexibility. We study denser solutions of the coarse-grained models with purely repulsive molecules (achievable by suitable salt conditions) and address the effect of packing and flexibility on dynamic and static behavior. Translational and rotational self-diffusivity is enhanced for more elastic models. Finally, we discuss a number of effective sphere sizes for the BSA molecule, which can be defined from its static and dynamic properties. Here, it is found that the effective sphere diameters lie between 4.9 and 6.1 nm, corresponding to a relative spread of about ±10% around a mean of 5.5 nm.
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| 9. |
- Hyde, William R., et al.
(författare)
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Microstructural and isotopic analysis of shocked monazite from the Hiawatha impact structure : development of porosity and its utility in dating impact craters
- 2024
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Ingår i: Contributions to Mineralogy and Petrology. - 0010-7999. ; 179:3
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Tidskriftsartikel (refereegranskat)abstract
- U–Pb geochronology of shocked monazite can be used to date hypervelocity impact events. Impact-induced recrystallisation and formation of mechanical twins in monazite have been shown to result in radiogenic Pb loss and thus constrain impact ages. However, little is known about the effect of porosity on the U–Pb system in shocked monazite. Here we investigate monazite in two impact melt rocks from the Hiawatha impact structure, Greenland by means of nano- and micrometre-scale techniques. Microstructural characterisation by scanning electron and transmission electron microscopy imaging and electron backscatter diffraction reveals shock recrystallisation, microtwins and the development of widespread micrometre- to nanometre-scale porosity. For the first time in shocked monazite, nanophases identified as cubic Pb, Pb3O4, and cerussite (PbCO3) were observed. We also find evidence for interaction with impact melt and fluids, with the formation of micrometre-scale melt-bearing channels, and the precipitation of the Pb-rich nanophases by dissolution–precipitation reactions involving pre-existing Pb-rich high-density clusters. To shed light on the response of monazite to shock metamorphism, high-spatial-resolution U–Pb dating by secondary ion mass spectrometry was completed. Recrystallised grains show the most advanced Pb loss, and together with porous grains yield concordia intercept ages within uncertainty of the previously established zircon U–Pb impact age attributed to the Hiawatha impact structure. Although porous grains alone yielded a less precise age, they are demonstrably useful in constraining impact ages. Observed relatively old apparent ages can be explained by significant retention of radiogenic lead in the form of widespread Pb nanophases. Lastly, we demonstrate that porous monazite is a valuable microtexture to search for when attempting to date poorly constrained impact structures, especially when shocked zircon or recrystallised monazite grains are not present.
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| 10. |
- Jax, Elinor, et al.
(författare)
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Health monitoring in birds using bio-loggers and whole blood transcriptomics
- 2021
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Monitoring and early detection of emerging infectious diseases in wild animals is of crucial global importance, yet reliable ways to measure immune status and responses are lacking for animals in the wild. Here we assess the usefulness of bio-loggers for detecting disease outbreaks in free-living birds and confirm detailed responses using leukocyte composition and large-scale transcriptomics. We simulated natural infections by viral and bacterial pathogens in captive mallards (Anas platyrhynchos), an important natural vector for avian influenza virus. We show that body temperature, heart rate and leukocyte composition change reliably during an acute phase immune response. Using genome-wide gene expression profiling of whole blood across time points we confirm that immunostimulants activate pathogen-specific gene regulatory networks. By reporting immune response related changes in physiological and behavioural traits that can be studied in free-ranging populations, we provide baseline information with importance to the global monitoring of zoonotic diseases.
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