1. |
- Campbell, PJ, et al.
(author)
-
Pan-cancer analysis of whole genomes
- 2020
-
In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
-
Journal article (peer-reviewed)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. |
- Poyatos, R., et al.
(author)
-
Global transpiration data from sap flow measurements: the SAPFLUXNET database
- 2021
-
In: Earth System Science Data. - : Copernicus GmbH. - 1866-3508 .- 1866-3516. ; 13:6, s. 2607-2649
-
Journal article (peer-reviewed)abstract
- Plant transpiration links physiological responses of vegetation to water supply and demand with hydrological, energy, and carbon budgets at the land-atmosphere interface. However, despite being the main land evaporative flux at the global scale, transpiration and its response to environmental drivers are currently not well constrained by observations. Here we introduce the first global compilation of whole-plant transpiration data from sap flow measurements (SAPFLUXNET, https://sapfluxnet.creaf.cat/, last access: 8 June 2021). We harmonized and quality-controlled individual datasets supplied by contributors worldwide in a semi-automatic data workflow implemented in the R programming language. Datasets include sub-daily time series of sap flow and hydrometeorological drivers for one or more growing seasons, as well as metadata on the stand characteristics, plant attributes, and technical details of the measurements. SAPFLUXNET contains 202 globally distributed datasets with sap flow time series for 2714 plants, mostly trees, of 174 species. SAPFLUXNET has a broad bioclimatic coverage, with woodland/shrubland and temperate forest biomes especially well represented (80 % of the datasets). The measurements cover a wide variety of stand structural characteristics and plant sizes. The datasets encompass the period between 1995 and 2018, with 50 % of the datasets being at least 3 years long. Accompanying radiation and vapour pressure deficit data are available for most of the datasets, while on-site soil water content is available for 56 % of the datasets. Many datasets contain data for species that make up 90 % or more of the total stand basal area, allowing the estimation of stand transpiration in diverse ecological settings. SAPFLUXNET adds to existing plant trait datasets, ecosystem flux networks, and remote sensing products to help increase our understanding of plant water use, plant responses to drought, and ecohydrological processes. SAPFLUXNET version 0.1.5 is freely available from the Zenodo repository (https://doi.org/10.5281/zenodo.3971689; Poyatos et al., 2020a). The "sapfluxnetr" R package - designed to access, visualize, and process SAPFLUXNET data - is available from CRAN.
|
|
3. |
- Mason, P, et al.
(author)
-
Octupole signatures in Ba-124,Ba-125
- 2005
-
In: Journal of Physics G. - : IOP Publishing. - 0954-3899 .- 1361-6471. ; 31:10, s. S1729-S1733
-
Journal article (peer-reviewed)abstract
- The gamma decay of the nuclei Ba-121,Ba-125 has been investigated with the EUROBALL array, using the reaction Ni-64+Ni-64 at E-beam = 255 and 261 MeV. Six new E1 transitions have been found in the nucleus Ba-125, suggesting a significant role of octupole correlations in the origin of its parity doublets. The J(pi) = 3(-) level of the nucleus Ba-124 has been identified for the first time. Its excitation energy is in very good agreement with a prediction based on a microscopic model including octupole interactions.
|
|
4. |
|
|
5. |
- Riley, M A, et al.
(author)
-
Beyond band termination in Er-157 and the search for wobbling excitations in strongly deformed Hf-174
- 2005
-
In: Journal of Physics G: Nuclear and Particle Physics. - : IOP Publishing. - 0954-3899 .- 1361-6471. ; 31:10, s. 1735-1740
-
Journal article (peer-reviewed)abstract
- High-spin terminating bands in heavy nuclei were first identified in nuclei around Er-158(90). While examples of special terminating states have been identified in a number of erbium isotopes, almost nothing is known about the states lying beyond band termination. In the present work the high-spin structure of Er-157 has been studied using the Gammasphere spectrometer. The subject of triaxial superdeformation and 'wobbling' modes in Lu nuclei has rightly attracted a great deal of attention. Very recently, four strongly or superdeformed (SD) sequences have been observed in Hf-174 and ultimate cranker calculations predict, such structures may have significant triaxial deformation. We have performed two experiments in an attempt to verify the possible triaxial nature of these bands. A lifetime measurement was performed to confirm the large (and similar) deformation of the bands. In addition, a high-statistics, thin-target experiment was run to search for linking transitions between the SD bands and possible wobbling modes.
|
|
6. |
- Riley, M. A., et al.
(author)
-
Observation of states beyond band termination in Er-156,Er-157,Er-158 and strongly deformed structures in Hf-173,Hf-174,Hf-175
- 2006
-
In: Physica Scripta. - 0031-8949. ; T125, s. 123-126
-
Journal article (peer-reviewed)abstract
- High-spin terminating bands in heavy nuclei were first identified in nuclei around Er-158(90). While examples of terminating states have been identified in a number of erbium isotopes, almost nothing is known about the states lying beyond band termination. In the present work, the high-spin structure of Er-156,Er-157,Er-158 has been studied using the Gammasphere spectrometer. The subject of triaxial superdeformation and 'wobbling' modes in Lu nuclei has rightly attracted a great deal of attention. Very recently four strongly or superdeformed (SD) sequences have been observed in Hf-174, and cranking calculations using the Ultimate Cranker code predict that such structures may have significant triaxial deformation. We have performed two experiments in an attempt to verify the possible triaxial nature of these bands. A lifetime measurement was performed to confirm the large (and similar) deformation of the bands. In addition, a high-statistics, thin-target experiment took place to search for linking transitions between the SD bands, possible wobbling modes, and new SD band structures.
|
|
7. |
|
|
8. |
|
|
9. |
|
|
10. |
- Ek, Weronica E, et al.
(author)
-
Polymorphisms in genes in the androgen pathway and risk of Barrett's esophagus and esophageal adenocarcinoma
- 2016
-
In: International Journal of Cancer. - : Wiley. - 0020-7136 .- 1097-0215. ; 138:5, s. 1146-1152
-
Journal article (peer-reviewed)abstract
- The strong male predominance in Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC) remains inadequately explained, but sex hormones might be involved. We hypothesized that single nucleotide polymorphisms (SNPs) in the androgen pathway influence risk of developing BE and EAC. This genetic-epidemiological analysis included 14 studies from Australia, Europe and North America. Polymorphisms in 16 genes coding for the androgen pathway were analyzed using a gene-based approach: versatile gene-based test association study. This method evaluates associations between a trait and all SNPs within a specific gene rather than each SNP marker individually as in a conventional GWAS. The data were stratified for sex, body-mass index, waist-to-hip ratio, tobacco smoking and gastroesophageal reflux status. Included were data from 1,508 EAC patients, 2,383 BE patients and 2,170 control participants. SNPs within the gene CYP17A1 were associated with risk of BE in the sexes combined (p=0.002) and in males (p=0.003), but not in females separately (p=0.3). This association was found in tobacco smokers (p=0.003) and in BE patients without reflux (p=0.004), but not in nonsmokers (p=0.2) or those with reflux (p=0.036). SNPs within JMJD1C were associated with risk of EAC in females (p=0.001). However, none of these associations replicated in a subsequent sample. Fourteen other genes studied did not reach statistically significant levels of association with BE, EAC or the combination of BE and EAC, after correcting for the number of genes included in the analysis. In conclusion, genetic variants in the androgen-related genes CYP17A1 and JMJD1C might be associated with risk of BE and EAC, respectively, but replication data with larger sample sizes are needed.
|
|
11. |
|
|
12. |
- Haeni, M., et al.
(author)
-
Winter respiratory C losses provide explanatory power for net ecosystem productivity
- 2017
-
In: Journal of Geophysical Research - Biogeosciences. - 2169-8953. ; 122:1, s. 243-260
-
Journal article (peer-reviewed)abstract
- Accurate predictions of net ecosystem productivity (NEPc) of forest ecosystems are essential for climate change decisions and requirements in the context of national forest growth and greenhouse gas inventories. However, drivers and underlying mechanisms determining NEPc (e.g., climate and nutrients) are not entirely understood yet, particularly when considering the influence of past periods. Here we explored the explanatory power of the compensation day (cDOY)-defined as the day of year when winter net carbon losses are compensated by spring assimilation-for NEPc in 26 forests in Europe, North America, and Australia, using different NEPc integration methods. We found cDOY to be a particularly powerful predictor for NEPc of temperate evergreen needleleaf forests (R2=0.58) and deciduous broadleaf forests (R2=0.68). In general, the latest cDOY correlated with the lowest NEPc. The explanatory power of cDOY depended on the integration method for NEPc, forest type, and whether the site had a distinct winter net respiratory carbon loss or not. The integration methods starting in autumn led to better predictions of NEPc from cDOY then the classical calendar method starting 1 January. Limited explanatory power of cDOY for NEPc was found for warmer sites with no distinct winter respiratory loss period. Our findings highlight the importance of the influence of winter processes and the delayed responses of previous seasons' climatic conditions on current year's NEPc. Such carry-over effects may contain information from climatic conditions, carbon storage levels, and hydraulic traits of several years back in time.
|
|
13. |
- Joss, D. T., et al.
(author)
-
Yrast states and band crossings in the neutron-deficient platinum isotopes Pt169-173
- 2006
-
In: Physical Review C. Nuclear Physics. - 0556-2813 .- 1089-490X. ; 74:1
-
Journal article (peer-reviewed)abstract
- The yrast states in the light platinum isotopes Pt169-173 have been investigated in a recoil-decay tagging experiment using the JUROGAM gamma-ray spectrometer in conjunction with the RITU gas-filled recoil separator and the GREAT tagging spectrometer. Gamma-ray transitions have been established for the first time in the odd-N isotopes, Pt-169 and Pt-173, and the yrast sequences in Pt-170 and Pt-172 have been extended. We discuss the possibility that the weakly deformed yrast structures of Pt-170, Pt-172, and Pt-173 are crossed by a deformed intruder configuration at spin similar to 8h.
|
|
14. |
|
|
15. |
|
|
16. |
|
|
17. |
|
|
18. |
|
|
19. |
- Lagergren, K., et al.
(author)
-
Polymorphisms in Genes of Relevance for Oestrogen and Oxytocin Pathways and Risk of Barrett's Oesophagus and Oesophageal Adenocarcinoma: A Pooled Analysis from the BEACON Consortium
- 2015
-
In: Plos One. - : Public Library of Science (PLoS). - 1932-6203. ; 10:9
-
Journal article (peer-reviewed)abstract
- Background The strong male predominance in oesophageal adenocarcinoma (OAC) and Barrett's oesophagus (BO) continues to puzzle. Hormonal influence, e.g. oestrogen or oxytocin, might contribute. This genetic-epidemiological study pooled 14 studies from three continents, Australia, Europe, and North America. Polymorphisms in 3 key genes coding for the oestrogen pathway (receptor alpha (ESR1), receptor beta (ESR2), and aromatase (CYP19A1)), and 3 key genes of the oxytocin pathway (the oxytocin receptor (OXTR), oxytocin protein (OXT), and cyclic ADP ribose hydrolase glycoprotein (CD38)), were analysed using a gene-based approach, versatile gene-based test association study (VEGAS). Among 1508 OAC patients, 2383 BO patients, and 2170 controls, genetic variants within ESR1 were associated with BO in males (p = 0.0058) and an increased risk of OAC and BO combined in males (p = 0.0023). Genetic variants within OXTR were associated with an increased risk of BO in both sexes combined (p = 0.0035) and in males (p = 0.0012). We followed up these suggestive findings in a further smaller data set, but found no replication. There were no significant associations between the other 4 genes studied and risk of OAC, BO, separately on in combination, in males and females combined or in males only. Genetic variants in the oestrogen receptor alpha and the oxytocin receptor may be associated with an increased risk of BO or OAC, but replication in other large samples are needed.
|
|
20. |
|
|
21. |
|
|
22. |
- Luyssaert, S., et al.
(author)
-
CO2 balance of boreal, temperate, and tropical forests derived from a global database
- 2007
-
In: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 13:12, s. 2509-2537
-
Research review (peer-reviewed)abstract
- Terrestrial ecosystems sequester 2.1 Pg of atmospheric carbon annually. A large amount of the terrestrial sink is realized by forests. However, considerable uncertainties remain regarding the fate of this carbon over both short and long timescales. Relevant data to address these uncertainties are being collected at many sites around the world, but syntheses of these data are still sparse. To facilitate future synthesis activities, we have assembled a comprehensive global database for forest ecosystems, which includes carbon budget variables (fluxes and stocks), ecosystem traits (e.g. leaf area index, age), as well as ancillary site information such as management regime, climate, and soil characteristics. This publicly available database can be used to quantify global, regional or biome-specific carbon budgets; to re-examine established relationships; to test emerging hypotheses about ecosystem functioning [e.g. a constant net ecosystem production (NEP) to gross primary production (GPP) ratio]; and as benchmarks for model evaluations. In this paper, we present the first analysis of this database. We discuss the climatic influences on GPP, net primary production (NPP) and NEP and present the CO2 balances for boreal, temperate, and tropical forest biomes based on micrometeorological, ecophysiological, and biometric flux and inventory estimates. Globally, GPP of forests benefited from higher temperatures and precipitation whereas NPP saturated above either a threshold of 1500 mm precipitation or a mean annual temperature of 10 degrees C. The global pattern in NEP was insensitive to climate and is hypothesized to be mainly determined by nonclimatic conditions such as successional stage, management, site history, and site disturbance. In all biomes, closing the CO2 balance required the introduction of substantial biome-specific closure terms. Nonclosure was taken as an indication that respiratory processes, advection, and non-CO2 carbon fluxes are not presently being adequately accounted for.
|
|
23. |
|
|
24. |
|
|
25. |
|
|