| 1. |
- Campbell, PJ, et al.
(author)
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Pan-cancer analysis of whole genomes
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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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.
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| 2. |
- Burrascano, S., et al.
(author)
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Where are we now with European forest multi-taxon biodiversity and where can we head to?
- 2023
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In: Biological Conservation. - 0006-3207. ; 284
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Journal article (peer-reviewed)abstract
- The European biodiversity and forest strategies rely on forest sustainable management (SFM) to conserve forest biodiversity. However, current sustainability assessments hardly account for direct biodiversity indicators. We focused on forest multi-taxon biodiversity to: i) gather and map the existing information; ii) identify knowledge and research gaps; iii) discuss its research potential. We established a research network to fit data on species, standing trees, lying deadwood and sampling unit description from 34 local datasets across 3591 sampling units. A total of 8724 species were represented, with the share of common and rare species varying across taxonomic classes: some included many species with several rare ones (e.g., Insecta); others (e.g., Bryopsida) were repre-sented by few common species. Tree-related structural attributes were sampled in a subset of sampling units (2889; 2356; 2309 and 1388 respectively for diameter, height, deadwood and microhabitats). Overall, multi-taxon studies are biased towards mature forests and may underrepresent the species related to other develop-mental phases. European forest compositional categories were all represented, but beech forests were over-represented as compared to thermophilous and boreal forests. Most sampling units (94%) were referred to a habitat type of conservation concern. Existing information may support European conservation and SFM stra-tegies in: (i) methodological harmonization and coordinated monitoring; (ii) definition and testing of SFM in-dicators and thresholds; (iii) data-driven assessment of the effects of environmental and management drivers on multi-taxon forest biological and functional diversity, (iv) multi-scale forest monitoring integrating in-situ and remotely sensed information.
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| 3. |
- Vergallo, A., et al.
(author)
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Association of plasma YKL-40 with brain amyloid-β levels, memory performance, and sex in subjective memory complainers
- 2020
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In: Neurobiology of Aging. - : Elsevier BV. - 0197-4580. ; 96, s. 22-32
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Journal article (peer-reviewed)abstract
- Neuroinflammation, a key early pathomechanistic alteration of Alzheimer's disease, may represent either a detrimental or a compensatory mechanism or both (according to the disease stage). YKL-40, a glycoprotein highly expressed in differentiated glial cells, is a candidate biomarker for in vivo tracking neuroinflammation in humans. We performed a longitudinal study in a monocentric cohort of cognitively healthy individuals at risk for Alzheimer's disease exploring whether age, sex, and the apolipoprotein E ε4 allele affect plasma YKL-40 concentrations. We investigated whether YKL-40 is associated with brain amyloid-β (Aβ) deposition, neuronal activity, and neurodegeneration as assessed via neuroimaging biomarkers. Finally, we investigated whether YKL-40 may predict cognitive performance. We found an age-associated increase of YKL-40 and observed that men display higher concentrations than women, indicating a potential sexual dimorphism. Moreover, YKL-40 was positively associated with memory performance and negatively associated with brain Aβ deposition (but not with metabolic signal). Consistent with translational studies, our results suggest a potentially protective effect of glia on incipient brain Aβ accumulation and neuronal homeostasis. © 2020 Elsevier Inc.
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| 5. |
- Verstraeten, A., et al.
(author)
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Effects of tree pollen on throughfall element fluxes in European forests
- 2023
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In: Biogeochemistry. - Göteborg : Springer. - 0168-2563 .- 1573-515X. ; 165:3, s. 311-325
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Journal article (peer-reviewed)abstract
- The effects of tree pollen on precipitation chemistry are not fully understood and this can lead to misinterpretations of element deposition in European forests. We investigated the relationship between forest throughfall (TF) element fluxes and the Seasonal Pollen Integral (SPIn) using linear mixed-effects modelling (LME). TF was measured in 1990-2018 during the main pollen season (MPS, arbitrary two months) in 61 managed, mostly pure, even-aged Fagus, Quercus, Pinus, and Picea stands which are part of the ICP Forests Level II network. The SPIn for the dominant tree genus was observed at 56 aerobiological monitoring stations in nearby cities. The net contribution of pollen was estimated as the TF flux in the MPS minus the fluxes in the preceding and succeeding months. In stands of Fagus and Picea, two genera that do not form large amounts of flowers every year, TF fluxes of potassium (K+), ammonium-nitrogen (NH4+-N), dissolved organic carbon (DOC), and dissolved organic nitrogen (DON) showed a positive relationship with SPIn. However- for Fagus- a negative relationship was found between TF nitrate-nitrogen (NO3--N) fluxes and SPIn. For Quercus and Pinus, two genera producing many flowers each year, SPIn displayed limited variability and no clear association with TF element fluxes. Overall, pollen contributed on average 4.1-10.6% of the annual TF fluxes of K+ > DOC > DON > NH4+--N with the highest contribution in Quercus > Fagus > Pinus > Picea stands. Tree pollen appears to affect TF inorganic nitrogen fluxes both qualitatively and quantitatively, acting as a source of NH4+--N and a sink of NO3--N. Pollen appears to play a more complex role in nutrient cycling than previously thought.
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| 8. |
- Yakneen, S, et al.
(author)
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Butler enables rapid cloud-based analysis of thousands of human genomes
- 2020
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In: Nature biotechnology. - : Springer Science and Business Media LLC. - 1546-1696 .- 1087-0156. ; 38:3, s. 288-
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Journal article (peer-reviewed)abstract
- We present Butler, a computational tool that facilitates large-scale genomic analyses on public and academic clouds. Butler includes innovative anomaly detection and self-healing functions that improve the efficiency of data processing and analysis by 43% compared with current approaches. Butler enabled processing of a 725-terabyte cancer genome dataset from the Pan-Cancer Analysis of Whole Genomes (PCAWG) project in a time-efficient and uniform manner.
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| 10. |
- Borsato, M., et al.
(author)
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Unleashing the full power of LHCb to probe stealth new physics
- 2022
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In: Reports on Progress in Physics. - : IOP Publishing. - 0034-4885 .- 1361-6633. ; 85:2
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Journal article (peer-reviewed)abstract
- In this paper, we describe the potential of the LHCb experiment to detect stealth physics. This refers to dynamics beyond the standard model that would elude searches that focus on energetic objects or precision measurements of known processes. Stealth signatures include long-lived particles and light resonances that are produced very rarely or together with overwhelming backgrounds. We will discuss why LHCb is equipped to discover this kind of physics at the Large Hadron Collider and provide examples of well-motivated theoretical models that can be probed with great detail at the experiment.
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