| 1. |
- Kanai, M, et al.
(författare)
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- 2023
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swepub:Mat__t
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| 2. |
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| 3. |
- 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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| 4. |
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| 5. |
- Cossarizza, A., et al.
(författare)
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Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)
- 2019
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Ingår i: European Journal of Immunology. - : Wiley. - 0014-2980 .- 1521-4141. ; 49:10, s. 1457-1973
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Tidskriftsartikel (refereegranskat)abstract
- These guidelines are a consensus work of a considerable number of members of the immunology and flow cytometry community. They provide the theory and key practical aspects of flow cytometry enabling immunologists to avoid the common errors that often undermine immunological data. Notably, there are comprehensive sections of all major immune cell types with helpful Tables detailing phenotypes in murine and human cells. The latest flow cytometry techniques and applications are also described, featuring examples of the data that can be generated and, importantly, how the data can be analysed. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid, all written and peer-reviewed by leading experts in the field, making this an essential research companion.
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| 6. |
- Abgrall, N., et al.
(författare)
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The large enriched germanium experiment for neutrinoless double beta decay (LEGEND)
- 2017
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Ingår i: AIP Conference Proceedings. - : Author(s). - 1551-7616 .- 0094-243X. ; 1894
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Konferensbidrag (refereegranskat)abstract
- The observation of neutrinoless double-beta decay (0νββ) would show that lepton number is violated, reveal that neu-trinos are Majorana particles, and provide information on neutrino mass. A discovery-capable experiment covering the inverted ordering region, with effective Majorana neutrino masses of 15 - 50 meV, will require a tonne-scale experiment with excellent energy resolution and extremely low backgrounds, at the level of ∼0.1 count /(FWHM·t·yr) in the region of the signal. The current generation 76Ge experiments GERDA and the Majorana Demonstrator, utilizing high purity Germanium detectors with an intrinsic energy resolution of 0.12%, have achieved the lowest backgrounds by over an order of magnitude in the 0νββ signal region of all 0νββ experiments. Building on this success, the LEGEND collaboration has been formed to pursue a tonne-scale 76Ge experiment. The collaboration aims to develop a phased 0νββ experimental program with discovery potential at a half-life approaching or at 1028 years, using existing resources as appropriate to expedite physics results.
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| 7. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 8. |
- Ma, Y. M., et al.
(författare)
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Implementation of trait-based ozone plant sensitivity in the YaleInteractive terrestrial Biosphere model v1.0 to assess global vegetationdamage
- 2023
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Ingår i: Geoscientific Model Development. - 1991-959X. ; 16:8, s. 2261-2276
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Tidskriftsartikel (refereegranskat)abstract
- A major limitation in modeling global ozone (O-3) vegetation damage has long been the reliance on empirical O-3 sensitivity parameters derived from a limited number of species and applied at the level of plant functional types (PFTs), which ignore the large interspecific variations within the same PFT. Here, we present a major advance in large-scale assessments of O-3 plant injury by linking the trait leaf mass per area (LMA) and plant O-3 sensitivity in a broad and global perspective. Application of the new approach and a global LMA map in a dynamic global vegetation model reasonably represents the observed interspecific responses to O-3 with a unified sensitivity parameter for all plant species. Simulations suggest a contemporary global mean reduction of 4.8% in gross primary productivity by O-3, with a range of 1.1 %-12.6% for varied PFTs. Hotspots with damage > 10% are found in agricultural areas in the eastern US, western Europe, eastern China, and India, accompanied by moderate to high levels of surface O-3. Furthermore, we simulate the distribution of plant sensitivity to O-3, which is highly linked with the inherent leaf trait trade-off strategies of plants, revealing high risks for fast-growing species with low LMA, such as crops, grasses, and deciduous trees.
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| 9. |
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| 10. |
- Wang, Z. B., et al.
(författare)
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Characteristics of regional new particle formation in urban and regional background environments in the North China Plain
- 2013
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Ingår i: Atmos. Chem. Phys.. - : Copernicus Publications. - 1680-7324. ; 13:24, s. 12495-12506
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Tidskriftsartikel (refereegranskat)abstract
- Long-term measurements of particle number size distributions were carried out both at an urban background site (Peking University, PKU) and a regional Global Atmospheric Watch station (Shangdianzi, SDZ) from March to November in 2008. In total, 52 new particle formation (NPF) events were observed simultaneously at both sites, indicating that this is a regional phenomenon in the North China Plain. On average, the mean condensation sink value before the nucleation events started was 0.025 s−1 in the urban environment, which was 1.6 times higher than that at regional site. However, higher particle formation and growth rates were observed at PKU (10.8 cm−3 s−1 and 5.2 nm h−1) compared with those at SDZ (4.9 cm−3 s−1 and 4.0 nm h−1). These results implied that precursors were much more abundant in the polluted urban environment. Different from the observations in cleaner environments, the background conditions of the observed particle homogeneous nucleation events in the North China Plain could be characterized as the co-existing of a stronger source of precursor gases and a higher condensational sink of pre-existing aerosol particles. Secondary aerosol formation following nucleation events results in an increase of particle mass concentration, particle light scattering coefficient, and cloud condensation nuclei (CCN) number concentration, with consequences on visibility, radiative effects, and air quality. Typical regional NPF events with significant particle nucleation rates and subsequent particle growth over a sufficiently long time period at both sites were chosen to investigate the influence of NPF on the number concentration of "potential" CCN. As a result, the NPF and the subsequent condensable growth increased the CCN number concentration in the North China Plain by factors in the range from 5.6 to 8.7. Moreover, the potential contribution of anthropogenic emissions to the CCN number concentration was more than 50%, to which more attention should be drawn in regional and global climate modeling, especially in the polluted urban areas.
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