| 1. |
- 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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| 2. |
- Jin, Shoko, et al.
(författare)
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The wide-field, multiplexed, spectroscopic facility WEAVE : Survey design, overview, and simulated implementation
- 2024
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press. - 0035-8711 .- 1365-2966. ; 530:3, s. 2688-2730
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Tidskriftsartikel (refereegranskat)abstract
- WEAVE, the new wide-field, massively multiplexed spectroscopic survey facility for the William Herschel Telescope, saw first light in late 2022. WEAVE comprises a new 2-deg field-of-view prime-focus corrector system, a nearly 1000-multiplex fibre positioner, 20 individually deployable 'mini' integral field units (IFUs), and a single large IFU. These fibre systems feed a dual-beam spectrograph covering the wavelength range 366-959nm at R similar to 5000, or two shorter ranges at . After summarizing the design and implementation of WEAVE and its data systems, we present the organization, science drivers, and design of a five- to seven-year programme of eight individual surveys to: (i) study our Galaxy's origins by completing Gaia's phase-space information, providing metallicities to its limiting magnitude for similar to 3 million stars and detailed abundances for similar to 1.5 million brighter field and open-cluster stars; (ii) survey similar to 0.4 million Galactic-plane OBA stars, young stellar objects, and nearby gas to understand the evolution of young stars and their environments; (iii) perform an extensive spectral survey of white dwarfs; (iv) survey similar to 400 neutral-hydrogen-selected galaxies with the IFUs; (v) study properties and kinematics of stellar populations and ionized gas in z < 0.5 cluster galaxies; (vi) survey stellar populations and kinematics in field galaxies at 0.3 less than or similar to z less than or similar to 0.7; (vii) study the cosmic evolution of accretion and star formation using >1 million spectra of LOFAR-selected radio sources; and (viii) trace structures using intergalactic/circumgalactic gas at z > 2. Finally, we describe the WEAVE Operational Rehearsals using the WEAVE Simulator.
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| 3. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 4. |
- Bakx, Tristan, et al.
(författare)
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Areas of high conservation value support specialist forest birds
- 2023
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Ingår i: Ecosphere. - 2150-8925. ; 14:6
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Tidskriftsartikel (refereegranskat)abstract
- Scientists have deemed existing protected areas in European forests insufficient to halt and reverse biodiversity loss resulting from ongoing intensification of management. In Sweden, protected areas are therefore complemented with the so-called areas of high conservation value (AHCVs), that is, landscapes encompassing both protected and assumed biodiversity-valuable areas as well as surrounding land, where managers should pay increased attention to biodiversity. However, it is not known whether AHCVs are chosen so that the species they are intended to benefit inhabit such AHCVs to a higher degree. We investigated whether the occurrence and abundance of bird species that may be particularly vulnerable to intense forest management were higher in Swedish forest landscapes proposed as AHCVs compared with other forest landscapes. To this end, we fitted a joint species distribution model to bird count data for 70 forest bird species from a standardized Swedish bird monitoring scheme. Twelve of the 20 forest specialists (60%) were detected to occur more often inside AHCVs than outside, whereas no forest specialist was less likely to occur inside AHCVs. For forest generalists, the corresponding figures were 28% and 18%, respectively. Six of 15 red-listed species (40%) were detectably more likely to occur inside AHCVs. The relationship between AHCV status of landscapes and the abundance of individual species was not as consistently negative or positive. The higher occurrence of specialists and threatened species inside AHCVs than outside of them suggests that if managed correctly, AHCVs are important habitat for a considerable part of the specialized forest avifauna in Sweden. We conclude that AHCVs represent an opportunity for designing green infrastructure benefitting Swedish forest biodiversity.
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| 5. |
- Bakx, Tristan R.M., et al.
(författare)
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Farmland birds occupying forest clear-cuts respond to both local and landscape features
- 2020
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Ingår i: Forest Ecology and Management. - : Elsevier BV. - 0378-1127. ; 478
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Tidskriftsartikel (refereegranskat)abstract
- Agricultural landscapes have changed fast in Europe, which has led to steep declines in farmland biodiversity. While this has differentially impacted “farmland species”, some of these seem to be able to use alternative man-made open habitats in forests, such as forest clear-cuts and powerline rights-of-way. We investigated the use of clear-cuts by two historically declining farmland birds, the Yellowhammer (Emberiza citrinella) and the Red-backed Shrike (Lanius collurio), to determine both local and landscape habitat characteristics of clear-cuts used for breeding. Among 101 clear-cuts visited in Scania, southern Sweden, 27% were occupied by Yellowhammers and 12% by Red-backed Shrikes. Yellowhammer occurrence in clear-cuts was positively related to local spruce cover (the planted tree species). There was also an interaction between clear-cut size and the proportion of farmland in the landscape, such that the positive effect of the proportion of farmland nearby was stronger for larger clear-cuts. Red-backed Shrike occurrence was positively related to clear-cut size and the local presence of piles of forest residues (tops and branches). The relation between occurrence and the proportion of clear-cuts in the landscape was positive for small clear-cuts and negative for larger ones. Yellowhammers and Red-backed shrikes are affected by both the local habitat structure in the clearcut and on the composition of the surrounding landscape, most likely because they use the clear-cut for nesting and the surroundings as complementary feeding habitat. To what extent clear-cuts as complementary breeding habitat to farmland may contribute to the conservation of Yellowhammers and Red-backed shrikes, as well as other farmland birds, is a promising path for future investigations.
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| 6. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 7. |
- Keskitalo, E. Carina H., 1974-, et al.
(författare)
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Case study and analogue methodologies in climate change vulnerability research
- 2010
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Ingår i: Wiley Interdisciplinary Reviews - Climate Change. - : John Wiley & Sons, Ltd. - 1757-7799 .- 1757-7780. ; 1:3, s. 374-392
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Tidskriftsartikel (refereegranskat)abstract
- Assessing vulnerability is an important component of human dimensions of climate change (HDCC) research. Vulnerability assessments identify and characterize who and what are sensitive to climatic risks and why, characterize adaptive capacity and its determinants, and identify opportunities for adaptation. This paper examines the importance of case study and analogue methodologies in vulnerability research, reviews the historical evolution of the two methodologies in the HDCC field, and identifies ways in which they can be used to increase our understanding of vulnerability. Case studies involve in-depth place-based research that focuses on a particular exposure unit (e.g., community, industry, etc.) to characterize vulnerability and its determinants. Temporal analogues use past and present experiences and responses to climatic variability, change and extremes to provide insights for vulnerability to climate change; spatial analogues involve conducting research in one region and identifying parallels to how another region might be affected by climate change. Vulnerability research that uses case studies and analogues can help to develop an understanding of the determinants of vulnerability and how they interact, and identify opportunities to reduce vulnerability and enhance adaptive capacity to current and future climate risks. This information can assist policy makers in developing adaptation plans and to mainstream climate change adaptation into other policy- and decision-making processes.
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| 8. |
- Martinez-Romera, Beatriz, et al.
(författare)
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Nordic Action for a Transformation to Low-carbon Shipping.
- 2017
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- The Paris Agreement aims to hold the increase in average global temperatures to well below 2°C above pre-industrial levels, and to pursue efforts to limit it to 1.5°C,1 but it does not refer specifically to emissions of greenhouse gases by the international maritime transport sector. This Report presents the findings of a project commissioned by the Nordic Council of Ministers through the Nordic Working Group for Global Climate Negotiations (NOAK) focusing on opportunities for Nordic countries to achieve a transition to low-carbon shipping globally, nationally and regionally. The Report is informed by a discussion paper released in November 2016 and a workshop convened in Malmö in December 2016, in which representatives of governments, businesses and the research community participated. The key findings of this Workshop Report are as follows.(1) Technology and finance.Promising technical and financial options are available to Nordic countries to support or lead a transition to low-carbon shipping. The Report presents these options in the form of a low-carbon road map for the sector (see Figure 1), which includes illustrative actions and outcomes concerning technological and operational measures, partnerships between the public and private sectors, and supporting policies and finance.(2) Public policy.Opportunities exist for Nordic countries to support and lead development of the public policies needed for transitions to low-carbon shipping. Internationally, Nordic countries are well positioned to lead efforts by the International Maritime Organization and others to define global targets for the sector and to build global ambition through partnerships with developing countries and flag registries.Outside the IMO, Nordic countries can catalyze transitions to low-carbon shipping through actions including market-based measures in Nordic countries, support for private-sector standards, low-carbon targets for Nordic fleets, arranging dialogue between stakeholders, including financiers and charterers, showcasing innovative Nordic practices, and building Nordic-led global partnerships such as “climate clubs”.(3) Collaboration.The actions described above are interdependent and interconnected. The success of a Nordic agenda for low-carbon shipping depends on the inclusion of all relevant stakeholders, the coordination of policies, and a holistic view of shipping and the important roles of Nordic governments, businesses and civil society within the sector.
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| 9. |
- Mora, C., et al.
(författare)
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Over half of known human pathogenic diseases can be aggravated by climate change
- 2022
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Ingår i: Nature Climate Change. - : Springer Science and Business Media LLC. - 1758-678X .- 1758-6798. ; 12, s. 869-875
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Tidskriftsartikel (refereegranskat)abstract
- It is relatively well accepted that climate change can affect human pathogenic diseases; however, the full extent of this risk remains poorly quantified. Here we carried out a systematic search for empirical examples about the impacts of ten climatic hazards sensitive to greenhouse gas (GHG) emissions on each known human pathogenic disease. We found that 58% (that is, 218 out of 375) of infectious diseases confronted by humanity worldwide have been at some point aggravated by climatic hazards; 16% were at times diminished. Empirical cases revealed 1,006 unique pathways in which climatic hazards, via different transmission types, led to pathogenic diseases. The human pathogenic diseases and transmission pathways aggravated by climatic hazards are too numerous for comprehensive societal adaptations, highlighting the urgent need to work at the source of the problem: reducing GHG emissions.
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| 10. |
- Pahlevan, Nima, et al.
(författare)
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ACIX-Aqua : A global assessment of atmospheric correction methods for Landsat-8 and Sentinel-2 over lakes, rivers, and coastal waters
- 2021
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Ingår i: Remote Sensing of Environment. - : Elsevier BV. - 0034-4257 .- 1879-0704. ; 258
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Tidskriftsartikel (refereegranskat)abstract
- Atmospheric correction over inland and coastal waters is one of the major remaining challenges in aquatic remote sensing, often hindering the quantitative retrieval of biogeochemical variables and analysis of their spatial and temporal variability within aquatic environments. The Atmospheric Correction Intercomparison Exercise (ACIX-Aqua), a joint NASA - ESA activity, was initiated to enable a thorough evaluation of eight state-of-the-art atmospheric correction (AC) processors available for Landsat-8 and Sentinel-2 data processing. Over 1000 radiometric matchups from both freshwaters (rivers, lakes, reservoirs) and coastal waters were utilized to examine the quality of derived aquatic reflectances ((rho) over cap (w)). This dataset originated from two sources: Data gathered from the international scientific community (henceforth called Community Validation Database, CVD), which captured predominantly inland water observations, and the Ocean Color component of AERONET measurements (AERONET-OC), representing primarily coastal ocean environments. This volume of data permitted the evaluation of the AC processors individually (using all the matchups) and comparatively (across seven different Optical Water Types, OWTs) using common matchups. We found that the performance of the AC processors differed for CVD and AERONET-OC matchups, likely reflecting inherent variability in aquatic and atmospheric properties between the two datasets. For the former, the median errors in (rho) over cap (w)(560) and (rho) over cap (w)(664) were found to range from 20 to 30% for best-performing processors. Using the AERONET-OC matchups, our performance assessments showed that median errors within the 15-30% range in these spectral bands may be achieved. The largest uncertainties were associated with the blue bands (25 to 60%) for best-performing processors considering both CVD and AERONET-OC assessments. We further assessed uncertainty propagation to the downstream products such as near-surface concentration of chlorophyll-a (Chla) and Total Suspended Solids (TSS). Using satellite matchups from the CVD along with in situ Chla and TSS, we found that 20-30% uncertainties in (rho) over cap (w)(490 <= lambda <= 743 nm) yielded 25-70% uncertainties in derived Chla and TSS products for top-performing AC processors. We summarize our results using performance matrices guiding the satellite user community through the OWT-specific relative performance of AC processors. Our analysis stresses the need for better representation of aerosols, particularly absorbing ones, and improvements in corrections for sky- (or sun-) glint and adjacency effects, in order to achieve higher quality downstream products in freshwater and coastal ecosystems.
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