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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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| 3. |
- Polme, S., et al.
(författare)
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FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles
- 2020
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Ingår i: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 105:1, s. 1-16
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Tidskriftsartikel (refereegranskat)abstract
- The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and Fun(Fun) together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold.
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| 5. |
- Amaechina, E., et al.
(författare)
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Policy Note: Policy Responses to Ensure Access to Water and Sanitation Services During COVID-19: Snapshots from the Environment for Development (EfD) Network
- 2020
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Ingår i: Water Economics and Policy. - : World Scientific Pub Co Pte Lt. - 2382-624X .- 2382-6258. ; 6:4
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Tidskriftsartikel (refereegranskat)abstract
- This policy note provides a snapshot of water and sanitation measures implemented by governments in response to the COVID-19 pandemic in 14 countries in the Global South: Costa Rica, El Salvador, Guatemala, Honduras, Nicaragua, Chile, Colombia, Ghana, Kenya, Nigeria, Panama, South Africa, Uganda and Vietnam. We find that many countries have taken action to stop utility disconnections due to non-payment. With the exception of Ghana and Vietnam, few countries are instituting new water subsidy programs, and are instead choosing to defer customers' bills for future payment, presumably when the pandemic recedes and households will be able to pay their bills. It is easier for the utilities' COVID-relief policies to target customers with piped connections who regularly receive bills. However, the situation for unconnected households appears more dire. Some countries (e.g., Ghana, Kenya, South Africa and Uganda) are attempting to provide unconnected households temporary access to water, but these households remain the most vulnerable. This health crisis has accentuated the importance of strong governance structures and resilient water service providers for dealing with external health, environmental and economic shocks.
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| 6. |
- Weisen, H., et al.
(författare)
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Isotope dependence of energy, momentum and particle confinement in tokamaks
- 2020
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Ingår i: Journal of Plasma Physics. - : Cambridge University Press. - 0022-3778 .- 1469-7807. ; 86:5
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Tidskriftsartikel (refereegranskat)abstract
- The isotope dependence of plasma transport will have a significant impact on the performance of future D-T experiments in JET and ITER and eventually on the fusion gain and economics of future reactors. In preparation for future D-T operation on JET, dedicated experiments and comprehensive transport analyses were performed in H, D and H-D mixed plasmas. The analysis of the data has demonstrated an unexpectedly strong and favourable dependence of the global confinement of energy, momentum and particles in ELMy H-mode plasmas on the atomic mass of the main ion species, the energy confinement time scaling as tau(E) similar to A(0.5) (Maggi et al., Plasma Phys. Control. Fusion, vol. 60, 2018, 014045; JET Team, Nucl. Fusion, vol. 39, 1999, pp. 1227-1244), i.e. opposite to the expectations based only on local gyro-Bohm (GB) scaling, tau(E) similar to A(-0.5), and stronger than in the commonly used H-mode scaling for the energy confinement (Saibene et al., Nucl. Fusion, vol. 39, 1999, 1133; ITER Physics Basis, Nucl. Fusion, vol. 39, 1999, 2175). The scaling of momentum transport and particle confinement with isotope mass is very similar to that of energy transport. Nonlinear local GENE gyrokinetic analysis shows that the observed anti-GB heat flux is accounted for if collisions, ExB shear and plasma dilution with low-Z impurities (Be-9) are included in the analysis (E and B are, respectively the electric and magnetic fields). For L-mode plasmas a weaker positive isotope scaling tau(E) similar to A(0.14) has been found in JET (Maggi et al., Plasma Phys. Control. Fusion, vol. 60, 2018, 014045), similar to ITER97-L scaling (Kaye et al., Nucl. Fusion, vol. 37, 1997, 1303). Flux-driven quasi-linear gyrofluid calculations using JETTO-TGLF in L-mode show that local GB scaling is not followed when stiff transport (as is generally the case for ion temperature gradient modes) is combined with an imposed boundary condition taken from the experiment, in this case predicting no isotope dependence. A dimensionless identity plasma pair in hydrogen and deuterium L-mode plasmas has demonstrated scale invariance, confirming that core transport physics is governed, as expected, by the 4 dimensionless parameters rho*, nu*, beta, q (normalised ion Larmor radius, collisionality, plasma pressure and safety factor) consistently with global quasi-linear gyrokinetic TGLF calculations (Maggi et al., Nucl. Fusion, vol. 59, 2019, 076028). We compare findings in JET with those in different devices and discuss the possible reasons for the different isotope scalings reported from different devices. The diversity of observations suggests that the differences may result not only from differences affecting the core, e.g. heating schemes, but are to a large part due to differences in device-specific edge and wall conditions, pointing to the importance of better understanding and controlling pedestal and edge processes.
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| 7. |
- Marin, Ida, et al.
(författare)
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Establishment of a clinical SPECT/CT protocol for imaging of(161)Tb
- 2020
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Ingår i: Ejnmmi Physics. - : Springer Science and Business Media LLC. - 2197-7364. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- Background It has been proposed, and preclinically demonstrated, that(161)Tb is a better alternative to(177)Lu for the treatment of small prostate cancer lesions due to its high emission of low-energy electrons.Tb-161 also emits photons suitable for single-photon emission computed tomography (SPECT) imaging. This study aims to establish a SPECT protocol for(161)Tb imaging in the clinic. Materials and methods Optimal settings using various gamma-camera collimators and energy windows were explored by imaging a Jaszczak phantom, including hollow-sphere inserts, filled with(161)Tb. The collimators examined were extended low-energy general purpose (ELEGP), medium-energy general purpose (MEGP), and low-energy high resolution (LEHR), respectively. In addition, three ordered subset expectation maximization (OSEM) algorithms were investigated: attenuation-corrected OSEM (A-OSEM); attenuation and dual- or triple-energy window scatter-corrected OSEM (AS-OSEM); and attenuation, scatter, and collimator-detector response-corrected OSEM (ASC-OSEM), where the latter utilized Monte Carlo-based reconstruction. Uniformity corrections, using intrinsic and extrinsic correction maps, were also investigated. Image quality was assessed by estimated recovery coefficients (RC), noise, and signal-to-noise ratio (SNR). Sensitivity was determined using a circular flat phantom. Results The best RC and SNR were obtained at an energy window between 67.1 and 82.1 keV. Ring artifacts, caused by non-uniformity, were removed with extrinsic uniformity correction for the energy window between 67.1 and 82.1 keV, but not with intrinsic correction. Analyzing the lower energy window between 48.9 and 62.9 keV, the ring artifacts remained after uniformity corrections. The recovery was similar for the different collimators when using a specific OSEM reconstruction. Recovery and SNR were highest for ASC-OSEM, followed by AS-OSEM and A-OSEM. When using the optimized parameter setting, the resolution of(161)Tb was higher than for(177)Lu (8.4 +/- 0.7 vs. 10.4 +/- 0.6 mm, respectively). The sensitivities for(161)Tb and(177)Lu were 7.41 and 8.46 cps/MBq, respectively. Conclusion SPECT with high resolution is feasible with(161)Tb; however, extrinsic uniformity correction is recommended to avoid ring artifacts. The LEHR collimator was the best choice of the three tested to obtain a high-resolution image. Due to the complex emission spectrum of low-energy photons, window-based scatter correction had a minor impact on the image quality compared to using attenuation correction only. On the other hand, performing attenuation, scatter, and collimator-detector correction clearly improved image quality. Based on these data, SPECT-based dosimetry for(161)Tb-labeled radiopharmaceuticals is feasible.
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