| 1. |
- Niemi, MEK, et al.
(author)
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- 2021
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swepub:Mat__t
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| 2. |
- Kanai, M, et al.
(author)
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- 2023
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swepub:Mat__t
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| 3. |
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| 4. |
- 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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| 5. |
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| 6. |
- Sumaila, U. Rashid, et al.
(author)
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WTO must ban harmful fisheries subsidies
- 2021
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 374:6567, s. 544-544
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Journal article (other academic/artistic)
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| 7. |
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| 8. |
- ODonnell, Michael, et al.
(author)
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Registered Replication Report: Dijksterhuis and van Knippenberg (1998)
- 2018
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In: Perspectives on Psychological Science. - : SAGE PUBLICATIONS LTD. - 1745-6916 .- 1745-6924. ; 13:2, s. 268-294
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Journal article (peer-reviewed)abstract
- Dijksterhuis and van Knippenberg (1998) reported that participants primed with a category associated with intelligence (professor) subsequently performed 13% better on a trivia test than participants primed with a category associated with a lack of intelligence (soccer hooligans). In two unpublished replications of this study designed to verify the appropriate testing procedures, Dijksterhuis, van Knippenberg, and Holland observed a smaller difference between conditions (2%-3%) as well as a gender difference: Men showed the effect (9.3% and 7.6%), but women did not (0.3% and -0.3%). The procedure used in those replications served as the basis for this multilab Registered Replication Report. A total of 40 laboratories collected data for this project, and 23 of these laboratories met all inclusion criteria. Here we report the meta-analytic results for those 23 direct replications (total N = 4,493), which tested whether performance on a 30-item general-knowledge trivia task differed between these two priming conditions (results of supplementary analyses of the data from all 40 labs, N = 6,454, are also reported). We observed no overall difference in trivia performance between participants primed with the professor category and those primed with the hooligan category (0.14%) and no moderation by gender.
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| 9. |
- Sakornsakolpat, Phuwanat, et al.
(author)
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Genetic landscape of chronic obstructive pulmonary disease identifies heterogeneous cell-type and phenotype associations
- 2019
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 51:3, s. 494-505
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Journal article (peer-reviewed)abstract
- Chronic obstructive pulmonary disease (COPD) is the leading cause of respiratory mortality worldwide. Genetic risk loci provide new insights into disease pathogenesis. We performed a genome-wide association study in 35,735 cases and 222,076 controls from the UK Biobank and additional studies from the International COPD Genetics Consortium. We identified 82 loci associated with P < 5 x 10-8; 47 of these were previously described in association with either COPD or population-based measures of lung function. Of the remaining 35 new loci, 13 were associated with lung function in 79,055 individuals from the SpiroMeta consortium. Using gene expression and regulation data, we identified functional enrichment of COPD risk loci in lung tissue, smooth muscle, and several lung cell types. We found 14 COPD loci shared with either asthma or pulmonary fibrosis. COPD genetic risk loci clustered into groups based on associations with quantitative imaging features and comorbidities. Our analyses provide further support for the genetic susceptibility and heterogeneity of COPD.
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| 11. |
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| 12. |
- Valassi, E., et al.
(author)
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High mortality within 90 days of diagnosis in patients with Cushing's syndrome: results from the ERCUSYN registry
- 2019
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In: European Journal of Endocrinology. - : Oxford University Press (OUP). - 0804-4643 .- 1479-683X. ; 181:5, s. 461-472
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Journal article (peer-reviewed)abstract
- Objective: Patients with Cushing's syndrome (CS) have increased mortality. The aim of this study was to evaluate the causes and time of death in a large cohort of patients with CS and to establish factors associated with increased mortality. Methods: In this cohort study, we analyzed 1564 patients included in the European Registry on CS (ERCUSYN); 1045 (67%) had pituitary-dependent CS, 385 (25%) adrenal-dependent CS, 89 (5%) had an ectopic source and 45 (3%) other causes. The median (IQR) overall follow-up time in ERCUSYN was 2.7 (1.2-5.5) years. Results: Forty-nine patients had died at the time of the analysis; 23 (47%) with pituitary-dependent CS, 6 (12%) with adrenal-dependent CS, 18 (37%) with ectopic CS and two (4%) with CS due to other causes. Of 42 patients whose cause of death was known, 15 (36%) died due to progression of the underlying disease, 13 (31%) due to infections, 7 (17%) due to cardiovascular or cerebrovascular disease and 2 due to pulmonary embolism. The commonest cause of death in patients with pituitary-dependent CS and adrenal-dependent CS were infectious diseases (n = 8) and progression of the underlying tumor (n = 10) in patients with ectopic CS. Patients who had died were older and more often males, and had more frequently muscle weakness, diabetes mellitus and ectopic CS, compared to survivors. Of 49 deceased patients, 22 (45%) died within 90 days from start of treatment and 5 (10%) before any treatment was given. The commonest cause of deaths in these 27 patients were infections (n = 10; 37%). In a regression analysis, age, ectopic CS and active disease were independently associated with overall death before and within 90 days from the start of treatment. Conclusion: Mortality rate was highest in patients with ectopic CS. Infectious diseases the commonest cause of death soon after diagnosis, emphasizing the need for careful vigilance at that time, especially in patients presenting with concomitant diabetes mellitus.
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| 13. |
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| 14. |
- Naidu, R., et al.
(author)
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Per- and poly-fluoroalkyl substances (PFAS) : Current status and research needs
- 2020
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In: Environmental Technology & Innovation. - : Elsevier BV. - 2352-1864. ; 19
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Journal article (peer-reviewed)abstract
- An expert workshop focusing on per- and poly-fluoroalkyl substances (PFAS) was held in Adelaide, South Australia, Australia in September 2019 following the 8th International Contaminated Site Remediation Conference — CleanUp 2019. The workshop was organised by the Cooperative Research Centre for Contamination and Remediation of the Environment (CRC CARE) and was chaired by Professor Ravi Naidu, CEO and Managing Director of CRC CARE and Director of the Global Centre for Environmental Remediation at the University of Newcastle, NSW. The purpose of the workshop, which was attended by more than 50 experts in the field of contaminated land assessment and management, was to discuss the current state of play and research needs relating to PFAS contaminated sites. This paper provides a summary of the discussions and conclusions and lists actions and needs that the expert group identified as critical for pursuing successful PFAS management and remedy approaches.This paper is intended to capture the shared information, comments, and current thinking related to PFAS challenges and research needs as identified by the group of expert participants; the write up is not intended to be a complete dissertation on the science and work that has been carried out. With a fast-evolving subject and increased government and public attention on PFAS presence in the environment, the group was convened with the objective of providing value in contributing to solutions to the PFAS challenges that are faced both in Australia and internationally. The text contained herein provides references to observations and methods that the experts drew on in their discussions and in support of their commentary; documentation of the original references was not provided, and the reader should consult the scientific literature if further information and confirmation of observations is required. Following a brief on the background to PFAS challenges, the paper focusses on research gaps identified by experts with focus on Australian soils and groundwater including climatic patterns, an overview of PFAS research in Australia with emphasis on:RegulatoryAnalytical considerationsEcological and Human Health RisksFate and TransportRemediation and Risk Management.
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| 15. |
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| 16. |
- Arrow, K. J., et al.
(author)
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Should Governments Use a Declining Discount Rate in Project Analysis?
- 2014
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In: Review of Environmental Economics and Policy. - : University of Chicago Press. - 1750-6816 .- 1750-6824. ; 8:2, s. 145-163
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Journal article (peer-reviewed)abstract
- Should governments use a discount rate that declines over time when evaluating the future benefits and costs of public projects? The argument for using a declining discount rate (DDR) is simple: if the discount rates that will be applied in the future are uncertain but positively correlated, and if the analyst can assign probabilities to these discount rates, then the result will be a declining schedule of certainty-equivalent discount rates. There is a growing empirical literature that estimates models of long-term interest rates and uses them to forecast the DDR schedule. However, this literature has been criticized because it lacks a connection to the theory of project evaluation. In benefit-cost analysis, the net benefits of a project in year t (in consumption units) are discounted to the present at the rate at which society would trade consumption in year t for consumption in the present. With simplifying assumptions, this leads to the Ramsey discounting formula, which results in a declining certainty-equivalent discount rate if the rate of growth in consumption is uncertain and if shocks to consumption are correlated over time. We conclude that the arguments in favor of a DDR are compelling and thus merit serious consideration by regulatory agencies in the United States.
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| 19. |
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| 20. |
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| 21. |
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| 22. |
- Aczel, Balazs, et al.
(author)
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Consensus-based guidance for conducting and reporting multi-analyst studies
- 2021
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In: eLIFE. - : eLife Sciences Publications. - 2050-084X. ; 10
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Journal article (peer-reviewed)abstract
- Any large dataset can be analyzed in a number of ways, and it is possible that the use of different analysis strategies will lead to different results and conclusions. One way to assess whether the results obtained depend on the analysis strategy chosen is to employ multiple analysts and leave each of them free to follow their own approach. Here, we present consensus-based guidance for conducting and reporting such multi-analyst studies, and we discuss how broader adoption of the multi-analyst approach has the potential to strengthen the robustness of results and conclusions obtained from analyses of datasets in basic and applied research.
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| 23. |
- Arrow, K., et al.
(author)
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Determining Benefits and Costs for Future Generations
- 2013
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In: Science. - 0036-8075. ; 341:6144, s. 349-350
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Journal article (peer-reviewed)abstract
- In economic project analysis, the rate at which future benefits and costs are discounted relative to current values often determines whether a project passes the benefit-cost test. This is especially true of projects with long time horizons, such as those to reduce greenhouse gas (GHG) emissions. Whether the benefits of climate policies, which can last for centuries, outweigh the costs, many of which are borne today, is especially sensitive to the rate at which future benefits are discounted. This is also true of other policies, e.g., affecting nuclear waste disposal or the construction of long-lived infrastructure
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| 24. |
- Biermann, F., et al.
(author)
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Navigating the Anthropocene: Improving Earth System Governance
- 2012
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In: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 335:6074, s. 1306-1307
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Journal article (other academic/artistic)abstract
- The United Nations conference in Rio de Janeiro in June is an important opportunity to improve the institutional framework for sustainable development.
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| 31. |
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| 32. |
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| 33. |
- Fallo, F., et al.
(author)
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Diagnosis and management of hypertension in patients with Cushing's syndrome: a position statement and consensus of the Working Group on Endocrine Hypertension of the European Society of Hypertension
- 2022
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In: Journal of hypertension. - : Ovid Technologies (Wolters Kluwer Health). - 0263-6352 .- 1473-5598. ; 40:11, s. 2085-2101
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Journal article (peer-reviewed)abstract
- Endogenous/exogenous Cushing's syndrome is characterized by a cluster of systemic manifestations of hypercortisolism, which cause increased cardiovascular risk. Its biological basis is glucocorticoid excess, acting on various pathogenic processes inducing cardiovascular damage. Hypertension is a common feature in Cushing's syndrome and may persist after normalizing hormone excess and discontinuing steroid therapy. In endogenous Cushing's syndrome, the earlier the diagnosis the sooner management can be employed to offset the deleterious effects of excess cortisol. Such management includes combined treatments directed against the underlying cause and tailored antihypertensive drugs aimed at controlling the consequences of glucocorticoid excess. Experts on endocrine hypertension and members of the Working Group on Endocrine Hypertension of the European Society of Hypertension (ESH) prepared this Consensus document, which summarizes the current knowledge in epidemiology, genetics, diagnosis, and treatment of hypertension in Cushing's syndrome.
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| 34. |
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| 35. |
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| 36. |
- Garg, Manik, et al.
(author)
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Tumour gene expression signature in primary melanoma predicts long-term outcomes
- 2021
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1
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Journal article (peer-reviewed)abstract
- Adjuvant systemic therapies are now routinely used following resection of stage III melanoma, however accurate prognostic information is needed to better stratify patients. We use differential expression analyses of primary tumours from 204 RNA-sequenced melanomas within a large adjuvant trial, identifying a 121 metastasis-associated gene signature. This signature strongly associated with progression-free (HR = 1.63, p = 5.24 × 10−5) and overall survival (HR = 1.61, p = 1.67 × 10−4), was validated in 175 regional lymph nodes metastasis as well as two externally ascertained datasets. The machine learning classification models trained using the signature genes performed significantly better in predicting metastases than models trained with clinical covariates (pAUROC = 7.03 × 10−4), or published prognostic signatures (pAUROC < 0.05). The signature score negatively correlated with measures of immune cell infiltration (ρ = −0.75, p < 2.2 × 10−16), with a higher score representing reduced lymphocyte infiltration and a higher 5-year risk of death in stage II melanoma. Our expression signature identifies melanoma patients at higher risk of metastases and warrants further evaluation in adjuvant clinical trials.
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| 37. |
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| 38. |
- Ohtani, S, et al.
(author)
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Simultaneous prenoon and postnoon observations of 3 field-aligned current systems from Viking and DMSP F7
- 1995
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In: Journal of Geophysical Research. - 0148-0227 .- 2156-2202. ; 100:A1, s. 119-136
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Journal article (peer-reviewed)abstract
- The spatial structure of dayside large-scale field-aligned current (FAG) systems is examined by using Viking and DMSP-F7 data. We focus on four events in which the satellites simultaneously observed postnoon and prenoon three FAC systems: the region 2, the region 1, and the mantle (referred to as midday region 0) systems, from equatorward to poleward. These events provide the most solid evidence to date that the midday region 0 system is a separate and unique FAC system, and is not an extension of the region 1 system from other local times. The events are examined comprehensively by making use of a multi-instrument data set, which includes magnetic field, particle flux, electric field, auroral UV image data from the satellites, and the Sondrestrom convection data. The results are summarized as follows: (1) Region 2 currents flow mostly in the CPS precipitation region, often overlapping with the BPS at their poleward edge. (2) The region 1 system is located in the core part of the auroral oval and is confined in a relatively narrow range in latitude which includes the convection reversal. The low-latitude boundary layer, possibly including the outer part of the plasma sheet, and the external cusp are the major source regions of dayside region 1 currents. (3) Midday region 0 currents flow on open field lines and are collocated with the shear of antisunward convection flows with velocities decreasing poleward. On the basis of these results we support the view that both prenoon and postnoon current systems consist of the three-sheet structure when the distortion of the convection pattern associated with interplanetary magnetic field (IMF) B-y is small and both morningside and eveningside convection cells are crescent-shaped. We also propose that the midday region 0 and a part of the region 1 systems are closely coupled to the same source.
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| 39. |
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| 40. |
- Valassi, E., et al.
(author)
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Worse Health-Related Quality of Life at long-term follow-up in patients with Cushing's disease than patients with cortisol producing adenoma. Data from the ERCUSYN
- 2018
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In: Clinical Endocrinology. - : Wiley. - 0300-0664. ; 88:6, s. 787-798
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Journal article (peer-reviewed)abstract
- ObjectiveHypercortisolism in Cushing's syndrome (CS) is associated with impaired health-related quality of life (HRQoL), which may persist despite remission. We used the data entered into the European Registry on Cushing's syndrome (ERCUSYN) to evaluate if patients with CS of pituitary origin (PIT-CS) have worse HRQoL, both before and after treatment than patients with adrenal causes (ADR-CS). MethodsData from 595 patients (492 women; 83%) who completed the CushingQoL and/or EQ-5D questionnaires at baseline and/or following treatment were analysed. ResultsAt baseline, HRQoL did not differ between PIT-CS (n=293) and ADR-CS (n=120) on both EuroQoL and CushingQoL. Total CushingQoL score in PIT-CS and ADR-CS was 4118 and 44 +/- 20, respectively (P=.7). At long-time follow-up (>1year after treatment) total CushingQoL score was however lower in PIT-CS than ADR-CS (56 +/- 20 vs 62 +/- 23; P=.045). In a regression analysis, after adjustment for baseline age, gender, remission status, duration of active CS, glucocorticoid dependency and follow-up time, no association was observed between aetiology and HRQoL. Remission was associated with better total CushingQoL score (P<.001), and older age at diagnosis with worse total score (P=.01). Depression at diagnosis was associated with worse total CushingQoL score at the last follow-up (P<.001). ConclusionPIT-CS patients had poorer HRQoL than ADR-CS at long-term follow-up, despite similar baseline scoring. After adjusting for remission status, no interaetiology differences in HRQoL scoring were found. Age and presence of depression at diagnosis of CS may be potential predictors of worse HRQoL regardless of CS aetiology.
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