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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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- Terpos, E., et al.
(författare)
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Early effects of IL-6 receptor inhibition on bone homeostasis: a pilot study in women with rheumatoid arthritis
- 2011
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Ingår i: Clinical and Experimental Rheumatology. - Pisa, Italy : Clinical and Experimental Rheumatology. - 0392-856X .- 1593-098X. ; 29:6, s. 921-925
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: A critical role of interleukin-6 (IL-6) in bone homeostasis has been suggested in experimental studies. We examined whether inhibition of IL-6 receptor in patients with rheumatoid arthritis (RA) results in early alterations of circulating markers of bone remodelling.Methods: Circulating levels of osteoprotegerin, receptor activator of nuclear factor-kappaB ligand (RANKL), Wnt signalling pathway inhibitors Dickkopf-1 (Dkk-1) and sclerostin, markers of bone resorption (C-terminal cross-linking telopeptide of collagen type-I (CTX), tartrate-resistant acid phosphatase isoform-5b) and bone formation (bone-specific alkaline-phosphatase, osteocalcin) were examined in 22 women with active RA before and after two monthly infusions of tocilizumab (8mg/kg each); 'healthy', non-osteopenic, 1:1 age-matched women served as controls.Results: At baseline, osteoprotegerin/RANKL ratio in patients was lower than controls by 5-fold; circulating osteoprotegerin correlated negatively with corresponding 28-joint-count disease activity scores and circulating RANKL correlated positively with C-reactive protein. Also, Dkk-1, sclerostin, CTX and osteocalcin levels were higher in RA than controls. After two months, osteoprotegerin/RANKL ratio increased, Dkk-1 decreased and sclerostin increased comparing to baseline; other markers did not change significantly. Increases of osteoprotegerin/RANKL ratio were more prominent in 10 patients who achieved remission or low disease activity after tocilizumab than in 12 patients who did not. In contrast, the significant alterations of both Wnt inhibitors were comparable between these patient subgroups.Conclusions: Anti-IL-6 therapy induced suppression of the inflammatory response affects rapidly the disrupted bone homeostasis in active RA. An additional, possibly specific, effect of IL-6 receptor inhibition on bone remodelling in humans should be further examined.
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- Meghini, C., et al.
(författare)
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ARIADNE: A Research Infrastructure for Archaeology
- 2017
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Ingår i: ACM Journal on Computing and Cultural Heritage. - : Association for Computing Machinery (ACM). - 1556-4673 .- 1556-4711. ; 10:3
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Tidskriftsartikel (refereegranskat)abstract
- Research e-infrastructures, digital archives, and data services have become important pillars of scientific enterprise that in recent decades have become ever more collaborative, distributed, and data intensive. The archaeological research community has been an early adopter of digital tools for data acquisition, organization, analysis, and presentation of research results of individual projects. However, the provision of e-infrastructure and services for data sharing, discovery, access, and (re) use have lagged behind. This situation is being addressed by ARIADNE, the Advanced Research Infrastructure for Archaeological Dataset Networking in Europe. This EU-funded network has developed an e-infrastructure that enables data providers to register and provide access to their resources (datasets, collections) through the ARIADNE data portal, facilitating discovery, access, and other services across the integrated resources. This article describes the current landscape of data repositories and services for archaeologists in Europe, and the issues that make interoperability between them difficult to realize. The results of the ARIADNE surveys on users' expectations and requirements are also presented. The main section of the article describes the architecture of the e-infrastructure, core services (data registration, discovery, and access), and various other extant or experimental services. The ongoing evaluation of the data integration and services is also discussed. Finally, the article summarizes lessons learned and outlines the prospects for the wider engagement of the archaeological research community in the sharing of data through ARIADNE.
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- Papazoglou, D., et al.
(författare)
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The Fatty Acid Amide Hydrolase (FAAH) Pro129Thr Polymorphism is not Associated with Severe Obesity in Greek Subjects
- 2008
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Ingår i: Hormone and Metabolic Research. - : Georg Thieme Verlag KG. - 1439-4286 .- 0018-5043. ; 40:12, s. 907-910
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Tidskriftsartikel (refereegranskat)abstract
- Fatty amid acid hydrolase (FAAH) has been implicated at both protein and gene level with obesity. An association between Pro129Thr variant of the FAAH gene and obesity has been described, but various studies have yielded conflicting results. Our aim was to determine whether this polymorphism is related to severe obesity and whether it confers a risk for variability of quantitative metabolic traits in a cohort of Greek obese Subjects. Two groups of severely obese Subjects (BMI >40 kg/m(2)) were studied: a group of 158 metabolically healthy and a group of 145 obese subjects with metabolic syndrome, which were compared to a Control group consisting of 121 lean individuals. We did not find any association between the Pro129Thr polymorphism with severe obesity in both subgroups of obese subjects, between these two subgroups (p = 0.11) or on basic anthropometric characteristics in the three groups. Statistically significant differences were found for glucose and HDL in metabolically healthy Subjects and HDL in the control group. The borderline significant p-values were not significant after correction for multiple testing. We were unable to find robust evidence of an association of the Pro 129Thr variant with severe obesity, and any related quantitative traits among the obese Greek Subjects examined.
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