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| 2. |
- Boija, Ann, et al.
(författare)
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CBP Regulates Recruitment and Release of Promoter-Proximal RNA Polymerase II
- 2017
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Ingår i: Molecular Cell. - : Elsevier BV. - 1097-2765 .- 1097-4164. ; 68:3, s. 491-503.e5
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Tidskriftsartikel (refereegranskat)abstract
- Transcription activation involves RNA polymerase II (Pol II) recruitment and release from the promoter into productive elongation, but how specific chromatin regulators control these steps is unclear. Here, we identify a novel activity of the histone acetyltransferase p300/CREB-binding protein (CBP) in regulating promoter-proximal paused Pol II. We find that Drosophila CBP inhibition results in "dribbling" of Pol II from the pause site to positions further downstream but impedes transcription through the +1 nucleosome genome-wide. Promoters strongly occupied by CBP and GAGA factor have high levels of paused Pol II, a unique chromatin signature, and are highly expressed regardless of cell type. Interestingly, CBP activity is rate limiting for Pol II recruitment to these highly paused promoters through an interaction with TFIIB but for transit into elongation by histone acetylation at other genes. Thus, CBP directly stimulates both Pol II recruitment and the ability to traverse the first nucleosome, thereby promoting transcription of most genes.
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| 3. |
- Botvinik-Nezer, Rotem, et al.
(författare)
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Variability in the analysis of a single neuroimaging dataset by many teams
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 582, s. 84-88
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Tidskriftsartikel (refereegranskat)abstract
- Data analysis workflows in many scientific domains have become increasingly complex and flexible. Here we assess the effect of this flexibility on the results of functional magnetic resonance imaging by asking 70 independent teams to analyse the same dataset, testing the same 9 ex-ante hypotheses(1). The flexibility of analytical approaches is exemplified by the fact that no two teams chose identical workflows to analyse the data. This flexibility resulted in sizeable variation in the results of hypothesis tests, even for teams whose statistical maps were highly correlated at intermediate stages of the analysis pipeline. Variation in reported results was related to several aspects of analysis methodology. Notably, a meta-analytical approach that aggregated information across teams yielded a significant consensus in activated regions. Furthermore, prediction markets of researchers in the field revealed an overestimation of the likelihood of significant findings, even by researchers with direct knowledge of the dataset(2-5). Our findings show that analytical flexibility can have substantial effects on scientific conclusions, and identify factors that may be related to variability in the analysis of functional magnetic resonance imaging. The results emphasize the importance of validating and sharing complex analysis workflows, and demonstrate the need for performing and reporting multiple analyses of the same data. Potential approaches that could be used to mitigate issues related to analytical variability are discussed. The results obtained by seventy different teams analysing the same functional magnetic resonance imaging dataset show substantial variation, highlighting the influence of analytical choices and the importance of sharing workflows publicly and performing multiple analyses.
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| 4. |
- Cole-Hunter, Thomas, et al.
(författare)
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Long-term air pollution exposure and Parkinson's disease mortality in a large pooled European cohort : An ELAPSE study
- 2023
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Ingår i: Environment International. - : Elsevier BV. - 0160-4120 .- 1873-6750. ; 171
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Tidskriftsartikel (refereegranskat)abstract
- Background: The link between exposure to ambient air pollution and mortality from cardiorespiratory diseases is well established, while evidence on neurodegenerative disorders including Parkinson’s Disease (PD) remains limited.Objective: We examined the association between long-term exposure to ambient air pollution and PD mortality in seven European cohorts.Methods: Within the project ‘Effects of Low-Level Air Pollution: A Study in Europe’ (ELAPSE), we pooled data from seven cohorts among six European countries. Annual mean residential concentrations of fine particulate matter (PM2.5), nitrogen dioxide (NO2), black carbon (BC), and ozone (O3), as well as 8 PM2.5 components (copper, iron, potassium, nickel, sulphur, silicon, vanadium, zinc), for 2010 were estimated using Europe-wide hybrid land use regression models. PD mortality was defined as underlying cause of death being either PD, secondary Parkinsonism, or dementia in PD. We applied Cox proportional hazard models to investigate the associations between air pollution and PD mortality, adjusting for potential confounders.Results: Of 271,720 cohort participants, 381 died from PD during 19.7 years of follow-up. In single-pollutant analyses, we observed positive associations between PD mortality and PM2.5 (hazard ratio per 5 µg/m3: 1.25; 95% confidence interval: 1.01–1.55), NO2 (1.13; 0.95–1.34 per 10 µg/m3), and BC (1.12; 0.94–1.34 per 0.5 × 10-5m-1), and a negative association with O3 (0.74; 0.58–0.94 per 10 µg/m3). Associations of PM2.5, NO2, and BC with PD mortality were linear without apparent lower thresholds. In two-pollutant models, associations with PM2.5 remained robust when adjusted for NO2 (1.24; 0.95–1.62) or BC (1.28; 0.96–1.71), whereas associations with NO2 or BC attenuated to null. O3 associations remained negative, but no longer statistically significant in models with PM2.5. We detected suggestive positive associations with the potassium component of PM2.5.Conclusion: Long-term exposure to PM2.5, at levels well below current EU air pollution limit values, may contribute to PD mortality.
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| 5. |
- Dearing, John A., et al.
(författare)
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Safe and just operating spaces for regional social-ecological systems
- 2014
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Ingår i: Global Environmental Change. - : Elsevier BV. - 0959-3780 .- 1872-9495. ; 28, s. 227-238
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Tidskriftsartikel (refereegranskat)abstract
- Humanity faces a major global challenge in achieving wellbeing for all, while simultaneously ensuring that the biophysical processes and ecosystem services that underpin wellbeing are exploited within scientifically informed boundaries of sustainability. We propose a framework for defining the safe and just operating space for humanity that integrates social wellbeing into the original planetary boundaries concept (Rockstrom et al., 2009a,b) for application at regional scales. We argue that such a framework can: (1) increase the policy impact of the boundaries concept as most governance takes place at the regional rather than planetary scale; (2) contribute to the understanding and dissemination of complexity thinking throughout governance and policy-making; (3) act as a powerful metaphor and communication tool for regional equity and sustainability. We demonstrate the approach in two rural Chinese localities where we define the safe and just operating space that lies between an environmental ceiling and a social foundation from analysis of time series drawn from monitored and palaeoecological data, and from social survey statistics respectively. Agricultural intensification has led to poverty reduction, though not eradicated it, but at the expense of environmental degradation. Currently, the environmental ceiling is exceeded for degraded water quality at both localities even though the least well-met social standards are for available piped water and sanitation. The conjunction of these social needs and environmental constraints around the issue of water access and quality illustrates the broader value of the safe and just operating space approach for sustainable development.
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| 6. |
- Kallio, Maarit Helena, et al.
(författare)
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The colour of maize : Visions of green growth and farmers perceptions in northern Laos
- 2019
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Ingår i: Land use policy. - : Elsevier BV. - 0264-8377 .- 1873-5754. ; 80, s. 185-194
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Tidskriftsartikel (refereegranskat)abstract
- The rapid expansion of hybrid maize in the uplands of northern Laos is viewed by the government as meeting policy aims related to green economic development. Yet, growing evidence of negative consequences of maize expansion are emerging. Based on farmers' perceptions, we study: (1) farmers' reasons for adopting and abandoning maize, and; (2) implications of commercial maize expansion on local livelihood security and inclusiveness (food supply, income, risk coping, and ability to join maize growing), and environmental sustainability (productivity, and soil and forest quality) over time (2013 and 2016). Results show that maize has advantages in terms of labour allocation, and it provides much-needed cash income. Yet, swidden is the main food provider and an essential safety net for unforeseen risks (including maize crop failures or price fluctuations). The way that maize was produced did not meet the criteria of green economic development due to its negative effects on the environment (soil and forest degradation) and socioeconomic sustainability (household differentiation, increased economic risks, debts, and food insecurity). By providing a local perspective, this study encourages a critical reflection of the underlying assumptions and conceptualization of the green economy approach in Laos, and argues for policies and measures that consider a more holistic perspective of human wellbeing and the environment.
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| 7. |
- Stjern, Camilla W., et al.
(författare)
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Response to marine cloud brightening in a multi-model ensemble
- 2018
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Ingår i: Atmospheric Chemistry And Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 18:2, s. 621-634
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Tidskriftsartikel (refereegranskat)abstract
- Here we show results from Earth system model simulations from the marine cloud brightening experiment G4cdnc of the Geoengineering Model Intercomparison Project (GeoMIP). The nine contributing models prescribe a 50% increase in the cloud droplet number concentration (CDNC) of low clouds over the global oceans in an experiment dubbed G4cdnc, with the purpose of counteracting the radiative forcing due to anthropogenic greenhouse gases under the RCP4.5 scenario. The model ensemble median effective radiative forcing (ERF) amounts to -1.9W m(-2), with a substantial inter-model spread of -0.6 to -2.5W m(-2). The large spread is partly related to the considerable differences in clouds and their representation between the models, with an underestimation of low clouds in several of the models. All models predict a statistically significant temperature decrease with a median of (for years 2020-2069) 0.96 [-0.17 to -1.21] K relative to the RCP4.5 scenario, with particularly strong cooling over low-latitude continents. Globally aver-aged there is a weak but significant precipitation decrease of -2.35 [-0.57 to -2.96]% due to a colder climate, but at low latitudes there is a 1.19% increase over land. This increase is part of a circulation change where a strong negative top-of-atmosphere (TOA) shortwave forcing over subtropical oceans, caused by increased albedo associated with the increasing CDNC, is compensated for by rising motion and positive TOA longwave signals over adjacent land regions.
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