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- Sherratt, K., et al.
(författare)
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Predictive performance of multi-model ensemble forecasts of COVID-19 across European nations
- 2023
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Ingår i: eLIFE. - : eLife Sciences Publications Ltd. - 2050-084X. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Methods: We used open-source tools to develop a public European COVID-19 Forecast Hub. We invited groups globally to contribute weekly forecasts for COVID-19 cases and deaths reported by a standardised source for 32 countries over the next 1–4 weeks. Teams submitted forecasts from March 2021 using standardised quantiles of the predictive distribution. Each week we created an ensemble forecast, where each predictive quantile was calculated as the equally-weighted average (initially the mean and then from 26th July the median) of all individual models’ predictive quantiles. We measured the performance of each model using the relative Weighted Interval Score (WIS), comparing models’ forecast accuracy relative to all other models. We retrospectively explored alternative methods for ensemble forecasts, including weighted averages based on models’ past predictive performance.Results: Over 52 weeks, we collected forecasts from 48 unique models. We evaluated 29 models’ forecast scores in comparison to the ensemble model. We found a weekly ensemble had a consistently strong performance across countries over time. Across all horizons and locations, the ensemble performed better on relative WIS than 83% of participating models’ forecasts of incident cases (with a total N=886 predictions from 23 unique models), and 91% of participating models’ forecasts of deaths (N=763 predictions from 20 models). Across a 1–4 week time horizon, ensemble performance declined with longer forecast periods when forecasting cases, but remained stable over 4 weeks for incident death forecasts. In every forecast across 32 countries, the ensemble outperformed most contributing models when forecasting either cases or deaths, frequently outperforming all of its individual component models. Among several choices of ensemble methods we found that the most influential and best choice was to use a median average of models instead of using the mean, regardless of methods of weighting component forecast models.Conclusions: Our results support the use of combining forecasts from individual models into an ensemble in order to improve predictive performance across epidemiological targets and populations during infectious disease epidemics. Our findings further suggest that median ensemble methods yield better predictive performance more than ones based on means. Our findings also highlight that forecast consumers should place more weight on incident death forecasts than incident case forecasts at forecast horizons greater than 2 weeks.
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- Thompson, PM, et al.
(författare)
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ENIGMA and global neuroscience: A decade of large-scale studies of the brain in health and disease across more than 40 countries
- 2020
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Ingår i: Translational psychiatry. - : Springer Science and Business Media LLC. - 2158-3188. ; 10:1, s. 100-
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Tidskriftsartikel (refereegranskat)abstract
- This review summarizes the last decade of work by the ENIGMA (Enhancing NeuroImaging Genetics through Meta Analysis) Consortium, a global alliance of over 1400 scientists across 43 countries, studying the human brain in health and disease. Building on large-scale genetic studies that discovered the first robustly replicated genetic loci associated with brain metrics, ENIGMA has diversified into over 50 working groups (WGs), pooling worldwide data and expertise to answer fundamental questions in neuroscience, psychiatry, neurology, and genetics. Most ENIGMA WGs focus on specific psychiatric and neurological conditions, other WGs study normal variation due to sex and gender differences, or development and aging; still other WGs develop methodological pipelines and tools to facilitate harmonized analyses of “big data” (i.e., genetic and epigenetic data, multimodal MRI, and electroencephalography data). These international efforts have yielded the largest neuroimaging studies to date in schizophrenia, bipolar disorder, major depressive disorder, post-traumatic stress disorder, substance use disorders, obsessive-compulsive disorder, attention-deficit/hyperactivity disorder, autism spectrum disorders, epilepsy, and 22q11.2 deletion syndrome. More recent ENIGMA WGs have formed to study anxiety disorders, suicidal thoughts and behavior, sleep and insomnia, eating disorders, irritability, brain injury, antisocial personality and conduct disorder, and dissociative identity disorder. Here, we summarize the first decade of ENIGMA’s activities and ongoing projects, and describe the successes and challenges encountered along the way. We highlight the advantages of collaborative large-scale coordinated data analyses for testing reproducibility and robustness of findings, offering the opportunity to identify brain systems involved in clinical syndromes across diverse samples and associated genetic, environmental, demographic, cognitive, and psychosocial factors.
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- Nordin, Joel Z., et al.
(författare)
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Ultrafiltration with size-exclusion liquid chromatography for high yield isolation of extracellular vesicles preserving intact biophysical and functional properties
- 2015
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Ingår i: Nanomedicine. - : Elsevier BV. - 1549-9634 .- 1549-9642. ; 11:4, s. 879-883
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Tidskriftsartikel (refereegranskat)abstract
- Extracellular vesicles (EVs) are natural nanoparticles that mediate intercellular transfer of RNA and proteins and are of great medical interest; serving as novel biomarkers and potential therapeutic agents. However, there is little consensus on the most appropriate method to isolate high-yield and high-purity EVs from various biological fluids. Here, we describe a systematic comparison between two protocols for EV purification: ultrafiltration with subsequent liquid chromatography (UF-LC) and differential ultracentrifugation (UC). A significantly higher EV yield resulted from UF-LC as compared to UC, without affecting vesicle protein composition. Importantly, we provide novel evidence that, in contrast to UC-purified EVs, the biophysical properties of UF-LC-purified EVs are preserved, leading toadifferent in vivo biodistribution, with less accumulation in lungs. Finally, we show that UF-LC is scalable and adaptable for EV isolation from complex media types such as stem cell media, which is of huge significance for future clinical applications involving EVs.
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- Saurer, Matthias, et al.
(författare)
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Spatial variability and temporal trends in water-use efficiency of European forests
- 2014
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Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 20:12, s. 3700-3712
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Tidskriftsartikel (refereegranskat)abstract
- The increasing carbon dioxide (CO2) concentration in the atmosphere in combination with climatic changes throughout the last century are likely to have had a profound effect on the physiology of trees: altering the carbon and water fluxes passing through the stomatal pores. However, the magnitude and spatial patterns of such changes in natural forests remain highly uncertain. Here, stable carbon isotope ratios from a network of 35 tree-ring sites located across Europe are investigated to determine the intrinsic water-use efficiency (iWUE), the ratio of photosynthesis to stomatal conductance from 1901 to 2000. The results were compared with simulations of a dynamic vegetation model (LPX-Bern 1.0) that integrates numerous ecosystem and land-atmosphere exchange processes in a theoretical framework. The spatial pattern of tree-ring derived iWUE of the investigated coniferous and deciduous species and the model results agreed significantly with a clear south-to-north gradient, as well as a general increase in iWUE over the 20th century. The magnitude of the iWUE increase was not spatially uniform, with the strongest increase observed and modelled for temperate forests in Central Europe, a region where summer soil-water availability decreased over the last century. We were able to demonstrate that the combined effects of increasing CO2 and climate change leading to soil drying have resulted in an accelerated increase in iWUE. These findings will help to reduce uncertainties in the land surface schemes of global climate models, where vegetation-climate feedbacks are currently still poorly constrained by observational data.
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- Steffen, Will, et al.
(författare)
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Stratigraphic and Earth System approaches to defining the Anthropocene
- 2016
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Ingår i: Earth's Future. - 2328-4277. ; 4:8, s. 324-345
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Forskningsöversikt (refereegranskat)abstract
- Stratigraphy provides insights into the evolution and dynamics of the Earth System over its long history. With recent developments in Earth System science, changes in Earth System dynamics can now be observed directly and projected into the near future. An integration of the two approaches provides powerful insights into the nature and significance of contemporary changes to Earth. From both perspectives, the Earth has been pushed out of the Holocene Epoch by human activities, with the mid-20th century a strong candidate for the start date of the Anthropocene, the proposed new epoch in Earth history. Here we explore two contrasting scenarios for the future of the Anthropocene, recognizing that the Earth System has already undergone a substantial transition away from the Holocene state. A rapid shift of societies toward the UN Sustainable Development Goals could stabilize the Earth System in a state with more intense interglacial conditions than in the late Quaternary climate regime and with little further biospheric change. In contrast, a continuation of the present Anthropocene trajectory of growing human pressures will likely lead to biotic impoverishment and a much warmer climate with a significant loss of polar ice.
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- Fairchild, Ian J., et al.
(författare)
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Tonian-Cryogenian boundary sections of Argyll, Scotland
- 2018
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Ingår i: Precambrian Research. - : Elsevier BV. - 0301-9268 .- 1872-7433. ; 319, s. 37-64
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Tidskriftsartikel (refereegranskat)abstract
- The Tonian-Cryogenian System boundary is to be defined at a GSSP (Global Boundary Stratigraphic Section and Point) beneath the first evidence of widespread glaciation. A candidate lies within the Dalradian Supergroup of Scotland and Ireland, which is least deformed and metamorphosed in Argyll, western Scotland. We present new stratigraphic profiles and interpretations from the Isle of Islay and the Garvellach Islands, update the chemostratigraphy of the Appin Group Tonian carbonates underlying the thick (ca. 1 km) glacigenic Port Askaig Formation (PAF) and demonstrate an environmental transition at the contact. The Appin Group forms a regionally extensive, > 4 km-thick, succession of limestones, shales and sandstones deposited on a marine shelf. On Islay, the upper part of the lithostratigraphy has been clarified by measuring and correlating two sections containing distinctive stratigraphic levels including molar tooth structure, oolite, stromatolitic dolomite and intraclastic microbial mounds. Significantly deeper erosion at the unconformity at the base of the overlying PAF is demonstrated in the southern section. Carbonate facies show a gradual decline in delta C-13(VPDB) from +5 to + 2 parts per thousand upwards. In NE Garbh Eileach (Garvellach Islands), a continuously exposed section of Appin Group carbonates, 70 m thick, here designated the Garbh Eileach Formation (GEF), lies conformably beneath the PAF. The GEF and the GEF-PAF boundary relationships are re -described with new sedimentological logs, petrological and stable isotope data. Interstratified limestone and dolomicrosparite with delta C-13 of -4 to -7 parts per thousand (a feature named the Garvellach anomaly, replacing the term Islay anomaly) are overlain by dolomite in which the isotope signature becomes weakly positive (up to +1 parts per thousand) upwards. Shallow subtidal conditions become peritidal upwards, with evidence of wave and storm activity. Gypsum pseudomorphs and subaerial exposure surfaces are common near the top of the GEF. The basal diamictite (D1) of the PAF is rich in carbonate clasts similar to slightly deeper water parts of the underlying succession. D1 is typically several metres thick with interstratified sandstone and conglomerate, but dies out laterally. Scattered siliciclastic coarse sandstone to pebble conglomerate with dropstones associated with soft -sediment deformation is interbedded with carbonate below and above D1. Dolomite beds with derived intraclasts and gypsum pseudomorphs are found above D1 (or equivalent position, where Dl is absent). Published and new Sr isotope studies, including successive leach data, demonstrate primary Tonian Sr-87/Sr-86 values of 0.7066-0.7069 on Islay, decreasing to 0.7064-0.7066 in the younger GEF limestones on the Garvellachs, with 1700-2700 ppm Sr. Other typically Tonian characteristics of the carbonates are the Sr-rich nature of limestones, molar tooth structure, and dolomitized peritidal facies with evidence of aridity. Seabed surveys suggesting uniformly-dipping strata and shallow borehole core material illustrate the potential for extending the Tonian record offshore of the Garvellachs. A candidate Tonian-Cryogenian GSSP is proposed on Garbh Eileach within the smooth delta C-13 profile at the cross-over to positive delta C-13 signatures, 4 m below the first occurrence of ice-rafted sediment and 9 m below the first diamictite. Although lacking radiometric constraints or stratigraphically significant biotas or biomarkers, the Scottish succession has a thick and relatively complete sedimentary record of glaciation, coherent carbon and strontium chemostratigraphy, lateral continuity of outcrops and 100% exposure at the proposed boundary interval.
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