| 1. |
- 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.
|
|
| 2. |
-
- 2019
-
Tidskriftsartikel (refereegranskat)
|
|
| 3. |
- Hernandez, E. M., et al.
(författare)
-
Absolute measurements of chlorine Cl+ cation single photoionization cross section
- 2015
-
Ingår i: Journal of Quantitative Spectroscopy & Radiative Transfer. - : Elsevier BV. - 0022-4073. ; 151, s. 217-223
-
Tidskriftsartikel (refereegranskat)abstract
- The photoionization of Cl+ leading to Cl2+ was measured in the photon energy range of 19.5-28.0 eV. A spectrum with a photon energy resolution of 15 meV normalized to absolute cross-section measurements is presented. The measurements were carried out by merging a Cl+ ion beam with a photon beam of highly monochromatic synchrotron radiation at the Advanced Light Source at Lawrence Berkeley National Laboratory. The measured photoionization of Cl+ consists of several autoionization resonances surperimposed on the direct photoionization signal. Most of the prominent resonances are assigned to members of Rydberg series originating from the singlet ground state and from metastable triplet levels within the ground-state configuration of Cl+. The direct ionization cross section is no larger than 12 Mb. (C) 2014 Elsevier Ltd. All rights reserved.
|
|
| 4. |
- Hinojosa, G., et al.
(författare)
-
Single photoionization of the Zn II ion in the photon energy range 17.5-90.0 eV: experiment and theory
- 2017
-
Ingår i: Monthly Notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 470:4, s. 4048-4060
-
Tidskriftsartikel (refereegranskat)abstract
- Measurements of the single-photoionization cross-section of Cu-like Zn+ ions are reported in the energy (wavelength) range 17.5 eV (708 angstrom) to 90 eV (138 angstrom). The measurements on this trans-Fe element were performed at the Advanced Light Source synchrotron radiation facility in Berkeley, California at a photon energy resolution of 17 meV using the photon-ion merged-beams end-station. Below 30 eV, the spectrum is dominated by excitation autoionizing resonance states. The experimental results are compared with large-scale photoionization cross-section calculations performed using a Dirac Coulomb R-matrix approximation. Comparisons are made with previous experimental studies, resonance states are identified and contributions from metastable states of Zn+ are determined.
|
|
| 5. |
- Hinojosa, G., et al.
(författare)
-
Single photoionization of the Zn II ion in the photon energy range 17.5-90.0 eV: experiment and theory
- 2017
-
Ingår i: Monthly Notices of the Royal Astronomical Society. - 0035-8711 .- 1365-2966. ; 470:4, s. 4048-4060
-
Tidskriftsartikel (refereegranskat)abstract
- Measurements of the single-photoionization cross-section of Cu-like Zn+ ions are reported in the energy (wavelength) range 17.5 eV (708 angstrom) to 90 eV (138 angstrom). The measurements on this trans-Fe element were performed at the Advanced Light Source synchrotron radiation facility in Berkeley, California at a photon energy resolution of 17 meV using the photon-ion merged-beams end-station. Below 30 eV, the spectrum is dominated by excitation autoionizing resonance states. The experimental results are compared with large-scale photoionization cross-section calculations performed using a Dirac Coulomb R-matrix approximation. Comparisons are made with previous experimental studies, resonance states are identified and contributions from metastable states of Zn+ are determined.
|
|
| 6. |
- Nahar, S. N., et al.
(författare)
-
Experimental and Theoretical Study of Photoionization of Cl III
- 2023
-
Ingår i: Atoms. - : MDPI AG. - 2218-2004. ; 11:2
-
Tidskriftsartikel (refereegranskat)abstract
- Photoionization of Cl III ions into Cl IV was studied theoretically using the ab initio relativistic Breit-Pauli R-matrix (BPRM) method and experimentally at the Advanced Light Source (ALS) synchrotron at the Lawrence Berkeley National Laboratory. A relative-ion-yield spectrum of Cl IV was measured with a photon energy resolution of 10 meV. The theoretical study was carried out using a large wave-function expansion of 45 levels of configurations 3s(2)3p(2), 3s3p(3), 3s(2)3p3d, 3s(2)3p4s, 3s3p(2)3d, and 3p(4). The resulting spectra are complex. We have compared the observed spectrum with photoionization cross sections (sigma PI) of the ground state 3s(2)3p(3)(S-4(3/2)o) and the seven lowest excited levels 3s(2)3p(3)(D-2(5/2)o), 3s(2)3p(3)(D-2(3/2)o), 3s(2)3p(3)(P-2(3/2)o), 3s(2)3p3(P-2(1/2)o), 3s(3)p(4)((4)P5/2), 3s(3)p(4)(P-4(3/2)) and 3s3p(4)(P-4(1/2)) of Cl III, as these can generate resonances within the energy range of the experiment. We were able to identify most of the resonances as belonging to various specific initial levels within the primary Cl III ion beam. Compared to the first five levels, resonant structures in the sigma PI of excited levels of 3s3p(4) appear to have a weaker presence. We have also produced combined theoretical spectra of the levels by convolving the cross sections with a Gaussian profile of experimental width and summing them using statistical weight factors. The theoretical and experimental features show good agreement with the first five levels of Cl III. These features are also expected to elucidate the recent observed spectra of Cl III by Sloan Digital Scan Survey project.
|
|
| 7. |
- Nahar, S. N., et al.
(författare)
-
Photoionization of P+: Experiment and theory
- 2017
-
Ingår i: Journal of Quantitative Spectroscopy and Radiative Transfer. - : Elsevier BV. - 0022-4073. ; 187, s. 215-223
-
Tidskriftsartikel (refereegranskat)abstract
- An experimental and theoretical study of the single photoionization cross section of the P+ cation of phosphorus is presented. Photoionization (PI) cross sections are instrumental for the determination of abundances in the interstellar medium. The experiment was performed by merging an ion beam with a photon beam. The photon beam was nearly monochromatic and had an energy resolution of 24 meV. Calculations were carried out using the Breit–Pauli R-matrix method. The combined study was developed in the photon energy interval from 18 eV (68.9 nm) to 50 eV (24.8 nm). Comparison between the measured and the calculated cross section shows good agreement in general and identifies features of the process and existence of states in the experimental beam. The present results should provide for more accurate modeling of P+. © 2016 Elsevier Ltd
|
|
| 8. |
- Aguilar, A., et al.
(författare)
-
Double photodetachment from the Cl[-]ion
- 2004
-
Ingår i: Physical Review A - Atomic, Molecular, and Optical Physics. - 2469-9926 .- 2469-9934. ; 69:2
-
Tidskriftsartikel (refereegranskat)abstract
- The correlated process involving the photodetachment of two electrons from the [Formula Presented] ion has been investigated over the photon energy range 20–45 eV. In the experiment, a beam of photons from the Advanced Light Source (ALS) was collinearly merged with a counterpropagating beam of [Formula Presented] ions from a sputter ion source. The [Formula Presented] ions produced in the interaction region were detected, and the normalized signal was used to monitor the relative cross section for the reaction. An absolute scale for the cross section was established by measuring the spatial overlap of the two beams and by determining the efficiency for collection and detection of the [Formula Presented] ions. The overall magnitude and shape of the measured cross section for this process agrees well with an R-matrix calculation. The calculation identifies the dominant mechanism leading to the production of the [Formula Presented] ion as being a direct nonresonant process involving the ejection of a pair of electrons from the valence shell. Less important is the indirect nonresonant process that involves the production and decay of core-excited and doubly excited states of the Cl atom in an intermediate step. Direct and indirect resonant mechanisms involving the excitation of a single [Formula Presented] core electron or more than one valence electron of the [Formula Presented] ion were found to be insignificant in the energy range studied.
|
|
| 9. |
- Ben, Rayana M.C., et al.
(författare)
-
Guidelines for sampling, measuring and reporting ionized magnesium in undiluted serum, plasma or blood : International Federation of Clinical Chemistry and Laboratory Medicine (IFCC)
- 2005
-
Ingår i: Clinical Chemistry and Laboratory Medicine. - 1434-6621 .- 1437-4331. ; 43:5, s. 564-569
-
Tidskriftsartikel (refereegranskat)abstract
- All analyzers with ion-selective electrodes for ionized magnesium (iMg) should yield comparable and unbiased results. The prerequisite to achieve this goal is to reach consensus on sampling, measurement and reporting. The recommended guidelines for sampling, measurement and reporting iMg in plasma ("plasma" refers to circulating plasma and the forms in which it is sampled: the plasma phase of anticoagulated whole blood, plasma separated from blood cells, or serum) or blood, referring to the substance concentration of iMg in the calibrants, will provide results for iMg that are approximately 3% greater than its true concentration, and 4% less than its true molality. Binding of magnesium to proteins and ligands in plasma and blood is pH-dependent. Therefore, pH should be simultaneously measured to allow adjustment of iMg concentration to pH 7.4. The substance concentration of iMg may be physiologically and consequently clinically more relevant than the substance concentration of total magnesium. © 2005 by Walter de Gruyter.
|
|
| 10. |
- Davis, V. T., et al.
(författare)
-
Photo-double detachment from the F- ion
- 2005
-
Ingår i: Journal of Physics B-Atomic Molecular and Optical Physics. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 38:14, s. 2579-2589
-
Tidskriftsartikel (refereegranskat)
|
|
