| 1. |
- 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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| 2. |
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| 3. |
- Jiang, Mingkai, et al.
(författare)
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The fate of carbon in a mature forest under carbon dioxide enrichment
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 580:7802, s. 227-231
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Tidskriftsartikel (refereegranskat)abstract
- Atmospheric carbon dioxide enrichment (eCO2) can enhance plant carbon uptake and growth1–5, thereby providing an important negative feedback to climate change by slowing the rate of increase of the atmospheric CO2 concentration6. Although evidence gathered from young aggrading forests has generally indicated a strong CO2 fertilization effect on biomass growth3–5, it is unclear whether mature forests respond to eCO2 in a similar way. In mature trees and forest stands7–10, photosynthetic uptake has been found to increase under eCO2 without any apparent accompanying growth response, leaving the fate of additional carbon fixed under eCO2 unclear4,5,7–11. Here using data from the first ecosystem-scale Free-Air CO2 Enrichment (FACE) experiment in a mature forest, we constructed a comprehensive ecosystem carbon budget to track the fate of carbon as the forest responded to four years of eCO2 exposure. We show that, although the eCO2 treatment of +150 parts per million (+38 per cent) above ambient levels induced a 12 per cent (+247 grams of carbon per square metre per year) increase in carbon uptake through gross primary production, this additional carbon uptake did not lead to increased carbon sequestration at the ecosystem level. Instead, the majority of the extra carbon was emitted back into the atmosphere via several respiratory fluxes, with increased soil respiration alone accounting for half of the total uptake surplus. Our results call into question the predominant thinking that the capacity of forests to act as carbon sinks will be generally enhanced under eCO2, and challenge the efficacy of climate mitigation strategies that rely on ubiquitous CO2 fertilization as a driver of increased carbon sinks in global forests.
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| 4. |
- Carmichael, Theron W., et al.
(författare)
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Two Intermediate-mass Transiting Brown Dwarfs from the TESS Mission
- 2020
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Ingår i: Astronomical Journal. - : American Astronomical Society. - 1538-3881 .- 0004-6256. ; 160:1
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Tidskriftsartikel (refereegranskat)abstract
- We report the discovery of two intermediate-mass transiting brown dwarfs (BDs), TOI-569b and TOI-1406b, from NASA's Transiting Exoplanet Survey Satellite mission. TOI-569b has an orbital period of P=.55604±0.00016 days, a mass of Mb = 64.1±1.9 MJ, and a radius of Rb = 0.75±0.02 RJ. Its host star, TOI-569, has a mass of Må = 1.21±0.05 M, a radius of Rå = 1.47±0.03 R, [Fe H 0.29 0.09] = + dex, and an effective temperature of Teff = 5768±10K. TOI-1406b has an orbital period of P=10.57415±0.00063 days, a mass of Mb = 46.0± 2.7 MJ, and a radius of Rb = 0.86±0.03 RJ. The host star for this BD has a mass of Må = 1.18±0.09 M, a radius of Rå = 1.35±0.03 R, [Fe/H] =-0.08± 0.09 dex, and an effective temperature of Teff = 6290±100 K. Both BDs are in circular orbits around their host stars and are older than 3 Gyr based on stellar isochrone models of the stars. TOI-569 is one of two slightly evolved stars known to host a transiting BD (the other being KOI-415). TOI-1406b is one of three known transiting BDs to occupy the mass range of 40-50 MJ and one of two to have a circular orbit at a period near 10 days (with the first being KOI-205b). Both BDs have reliable ages from stellar isochrones, in addition to their well-constrained masses and radii, making them particularly valuable as tests for substellar isochrones in the BD mass-radius diagram.
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| 6. |
- Roulet, Céline, et al.
(författare)
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Managing hypertension in frail oldest-old-The role of guideline use by general practitioners from 29 countries
- 2020
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 15:7
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The best management of hypertension in frail oldest-old (≥80 years of age) remains unclear and we still lack guidelines that provide specific recommendations. Our study aims to investigate guideline use in general practitioners (GPs) and to examine if guideline use relates to different decisions when managing hypertension in frail oldest-old. DESIGN/SETTING: Cross-sectional study among currently active GPs from 29 countries using a case-vignettes survey. METHODS: GPs participated in a survey with case-vignettes of frail oldest-olds varying in systolic blood pressure (SBP) levels and cardiovascular disease (CVD). GPs from 26 European countries and from Brazil, Israel and New Zealand were invited. We compared the percentage of GPs reporting using guidelines per country and further stratified on the most frequently mentioned guidelines. To adjust for patient characteristics (SBP, CVD and GPs' sex, years of experience, prevalence of oldest-old and location of their practice), we used a mixed-effects regression model accounting for clustering within countries. RESULTS: Overall, 2,543 GPs from 29 countries were included. 59.4% of them reported to use guidelines. Higher guideline use was found in female (p = 0.031) and less-experienced GPs (p<0.001). Across countries, we found a large variation in self-reported guideline use, ranging from 25% to 90% of the GPs, but there was no difference in hypertension treatment decisions in frail oldest-old patients between GPs that did not use and GPs that used guidelines, irrespective of the guidelines they used. CONCLUSION: Many GPs reported using guidelines to manage hypertension in frail oldest-old patients, however guideline users did not decide differently from non-users concerning hypertension treatment decisions. Instead of focusing on the fact if GPs use guidelines or not, we as a scientific community should put an emphasis on what guidelines suggest in frail and oldest-old patients.
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| 7. |
- Chowdary, Pratima, et al.
(författare)
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Modeling to Predict Factor VIII Levels Associated with Zero Bleeds in Patients with Severe Hemophilia A Initiated on Tertiary Prophylaxis
- 2020
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Ingår i: Thrombosis and Haemostasis. - : Georg Thieme Verlag KG. - 0340-6245 .- 2567-689X. ; 120:5, s. 728-736
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Tidskriftsartikel (refereegranskat)abstract
- Background: Factor VIII (FVIII) trough levels > 1 IU/dL in patients with severe hemophilia A receiving regular prophylaxis may optimize bleed protection. Objectives: In this post hoc analysis of patients receiving tertiary prophylaxis for approximately 1 year, the relationship between estimated FVIII levels and reported bleeds was investigated to predict the potential for zero bleeds. Methods: Sixty-three patients (median [range] age, 28 [7-59] years) with severe hemophilia A (229 bleeds) were included. FVIII levels at time of each bleed were estimated from single-dose individual pharmacokinetics. The highest estimated FVIII level at which patients experienced a bleed was considered the potentially effective trough level for that bleed type. Kaplan-Meier estimates of proportions of patients with no bleeds above certain estimated FVIII levels were determined. Those not experiencing a bleed in the trial were assumed to have a bleed at 0 IU/dL (pragmatic approach) or at their median trough level (conservative approach). Results: Kaplan-Meier estimates based on pragmatic approach predicted zero all bleeds, joint bleeds, and spontaneous joint bleeds in 1 year in 40, 43, and 63% of patients, respectively, when the potentially effective trough FVIII level was set at 1 IU/dL. Between 1 and 10 IU/dL, every 1 IU/dL rise in estimated FVIII level was associated with an additional 2% of patients having zero all bleeds. Conclusion: This post hoc analysis confirms benefits with trough levels of approximately 1 to 3 IU/dL in most patients starting tertiary prophylaxis; prophylaxis with higher trough levels may help patients to achieve zero bleeds.
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| 8. |
- Collins, Max, et al.
(författare)
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Optimal Design of a High Voltage High Frequency Transformer and Power Drive System for Long Pulse Modulators
- 2020
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Ingår i: 2019 IEEE Pulsed Power and Plasma Science, PPPS 2019. - 2158-4923 .- 2158-4915. - 9781538679692 ; 2019-June
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Konferensbidrag (refereegranskat)abstract
- The stacked multi-level (SML) klystron modulator topology has been suggested as an alternative to conventional pulse transformer based topologies in an attempt to improve output pulse performance and reduce system size for long pulse applications. In this topology, a power converter chain including a high frequency transformer generates the output pulse in a pulse modulation/demodulation scheme, eliminating the direct size-pulse length dependency while allowing higher degree of freedom in design. However, increased complexity necessitates careful consideration from a system perspective to ensure appropriate component selection and design. First, from the perspective of the semiconductor switches, the pulsed nature of the load must be taken into account. High modulator average and peak powers are combined into a power cycling problem where lifetime issues must be managed when selecting semiconductor technology and converter operating frequency. Simultaneously, these considerations are directly coupled to the design of the high voltage high frequency transformer, the largest component in the SML chain, key in reducing modulator footprint and volume. In addition, appropriate passive components (snubbers) must be chosen with respect to transformer leakage inductance, switching frequency and switch ratings to constrain voltage overshoot without deteriorating system efficiency. In this paper, these integrated design considerations are combined with a catalog of IGBT switches available on the market to form an optimization algorithm set to minimize transformer volume, indicative of system oil tank volume, while ensuring high system efficiency and long semiconductor lifetime. The tradeoffs between system efficiency and volume are studied. Finally, the algorithm is used to outline the design procedure for a system rated for pulse amplitude 115 kV / 100 A, pulse length 3.5 ms, pulse repetition rate 14 Hz, efficiency>91%, lifetime>25 years. The derived design is validated through circuit simulation, 3D finite element analysis, and experiments.
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| 9. |
- Lees, William, et al.
(författare)
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OGRDB : a reference database of inferred immune receptor genes
- 2020
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 48:D1, s. 964-970
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Tidskriftsartikel (refereegranskat)abstract
- High-throughput sequencing of the adaptive immune receptor repertoire (AIRR-seq) is providing unprecedented insights into the immune response to disease and into the development of immune disorders. The accurate interpretation of AIRR-seq data depends on the existence of comprehensive germline gene reference sets. Current sets are known to be incomplete and unrepresentative of the degree of polymorphism and diversity in human and animal populations. A key issue is the complexity of the genomic regions in which they lie, which, because of the presence of multiple repeats, insertions and deletions, have not proved tractable with short-read whole genome sequencing. Recently, tools and methods for inferring such gene sequences from AIRR-seq datasets have become available, and a community approach has been developed for the expert review and publication of such inferences. Here, we present OGRDB, the Open Germline Receptor Database (https://ogrdb.airr-community.org), a public resource for the submission, review and publication of previously unknown receptor germline sequences together with supporting evidence.
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| 10. |
- Viñuela, Ana, et al.
(författare)
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Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D
- 2020
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1, s. 4912-4912
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Tidskriftsartikel (refereegranskat)abstract
- Most signals detected by genome-wide association studies map to non-coding sequence and their tissue-specific effects influence transcriptional regulation. However, key tissues and cell-types required for functional inference are absent from large-scale resources. Here we explore the relationship between genetic variants influencing predisposition to type 2 diabetes (T2D) and related glycemic traits, and human pancreatic islet transcription using data from 420 donors. We find: (a) 7741 cis-eQTLs in islets with a replication rate across 44 GTEx tissues between 40% and 73%; (b) marked overlap between islet cis-eQTL signals and active regulatory sequences in islets, with reduced eQTL effect size observed in the stretch enhancers most strongly implicated in GWAS signal location; (c) enrichment of islet cis-eQTL signals with T2D risk variants identified in genome-wide association studies; and (d) colocalization between 47 islet cis-eQTLs and variants influencing T2D or glycemic traits, including DGKB and TCF7L2. Our findings illustrate the advantages of performing functional and regulatory studies in disease relevant tissues.
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