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- 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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- Bogota-Angel, G., et al.
(författare)
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Climate and geological change as drivers of Mauritiinae palm biogeography
- 2021
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Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 48:5, s. 1001-1022
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Tidskriftsartikel (refereegranskat)abstract
- Aim Forest composition and distribution are determined by a myriad of factors, including climate. As models of tropical rain forest, palms are often used as indicator taxa, particularly the Mauritiinae. We question, what characterizes the Mauritiinae pollen in the global fossil record? And when did the Mauritiinae become endemic to South America? Location Global tropics. Taxon Mauritiinae palms (Arecaceae: Lepidocaryeae). Methods Pollen trait data from extinct and extant Mauritiinae pollen were generated from light-, scanning-, and transmission electron microscopy. Statistical morphometric analysis was used to define species and their relationships to other Mauritiinae. We also compiled a comprehensive pollen database for extinct and extant Mauritiinae and mapped their global geographical distribution from Late Cretaceous to present, using GBIF and fossil data. Results Our morphometric analysis identified 18 species (11 extinct and seven extant), all exhibiting exine indentations, a synapomorphy of the subtribe. The fossil taxa and early divergent extant Lepidocaryum are all monosulcate, whereas the extant Mauritia and Mauritiella species are all monoulcerate. Paleobiogeographical maps of fossil Mauritiinae pollen occurrences suggest the taxon originated in equatorial Africa during the Cretaceous, and expanded their range to South America, and to India in the Paleocene. Range retraction started in the early Eocene with extirpation from India, and reduction in diversity in Africa culminating at the Eocene-Oligocene Transition (EOT). In contrast, in South America, the distribution is maintained, and since the Neogene Mauritiinae palms are mostly restricted to swampy, lowland habitats. Main conclusions Morphometric analysis shows that since their origin Mauritiinae pollen are relatively species poor, and Mauritiidites resembles Lepidocaryum. We also conclude that the biogeographical history of the Mauriitinae and, by extension, tropical forests was strongly affected by global climatic cooling events. In particular, the climate change at the EOT was a fundamental determinant of current tropical forest distribution.
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- Abedi-Ardekani, B, et al.
(författare)
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Morphological findings in frozen non-neoplastic kidney tissues of patients with kidney cancer from large-scale multicentric studies on renal cancer
- 2021
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Ingår i: Virchows Archiv : an international journal of pathology. - : Springer Science and Business Media LLC. - 1432-2307. ; 478:6, s. 1099-1107
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Tidskriftsartikel (refereegranskat)abstract
- There are unexplained geographical variations in the incidence of kidney cancer with the high rates reported in Baltic countries, as well as eastern and central Europe. Having access to a large and well-annotated collection of “tumor/non-tumor” pairs of kidney cancer patients from the Czech Republic, Romania, Serbia, UK, and Russia, we aimed to analyze the morphology of non-neoplastic renal tissue in nephrectomy specimens. By applying digital pathology, we performed a microscopic examination of 1012 frozen non-neoplastic kidney tissues from patients with renal cell carcinoma. Four components of renal parenchyma were evaluated and scored for the intensity of interstitial inflammation and fibrosis, tubular atrophy, glomerulosclerosis, and arterial wall thickening, globally called chronic renal parenchymal changes. Moderate or severe changes were observed in 54 (5.3%) of patients with predominance of occurrence in Romania (OR = 2.67, CI 1.07–6.67) and Serbia (OR = 4.37, CI 1.20–15.96) in reference to those from Russia. Further adjustment for comorbidities, tumor characteristics, and stage did not change risk estimates. In multinomial regression model, relative probability of non-glomerular changes was 5.22 times higher for Romania and Serbia compared to Russia. Our findings show that the frequency of chronic renal parenchymal changes, with the predominance of chronic interstitial nephritis pattern, in kidney cancer patients varies by country, significantly more frequent in countries located in central and southeastern Europe where the incidence of kidney cancer has been reported to be moderate to high. The observed association between these pathological features and living in certain geographic areas requires a larger population-based study to confirm this association on a large scale.
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- Wright, Gillian, et al.
(författare)
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The Mid-infrared Instrument for JWST and Its In-flight Performance
- 2023
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Ingår i: Publications of the Astronomical Society of the Pacific. - 0004-6280 .- 1538-3873. ; 135:1046
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Tidskriftsartikel (refereegranskat)abstract
- The Mid-Infrared Instrument (MIRI) extends the reach of the James Webb Space Telescope (JWST) to 28.5 μm. It provides subarcsecond-resolution imaging, high sensitivity coronagraphy, and spectroscopy at resolutions of λ/Δλ ∼ 100-3500, with the high-resolution mode employing an integral field unit to provide spatial data cubes. The resulting broad suite of capabilities will enable huge advances in studies over this wavelength range. This overview describes the history of acquiring this capability for JWST. It discusses the basic attributes of the instrument optics, the detector arrays, and the cryocooler that keeps everything at approximately 7 K. It gives a short description of the data pipeline and of the instrument performance demonstrated during JWST commissioning. The bottom line is that the telescope and MIRI are both operating to the standards set by pre-launch predictions, and all of the MIRI capabilities are operating at, or even a bit better than, the level that had been expected. The paper is also designed to act as a roadmap to more detailed papers on different aspects of MIRI.
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