| 1. |
- Weinstein, John N., et al.
(författare)
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The cancer genome atlas pan-cancer analysis project
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:10, s. 1113-1120
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Forskningsöversikt (refereegranskat)abstract
- The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. © 2013 Nature America, Inc. All rights reserved.
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| 2. |
- Hollestelle, Antoinette, et al.
(författare)
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No clinical utility of KRAS variant rs61764370 for ovarian or breast cancer
- 2016
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Ingår i: Gynecologic Oncology. - : Elsevier BV. - 0090-8258 .- 1095-6859. ; 141:2, s. 386-401
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Tidskriftsartikel (refereegranskat)abstract
- Objective Clinical genetic testing is commercially available for rs61764370, an inherited variant residing in a KRAS 3′ UTR microRNA binding site, based on suggested associations with increased ovarian and breast cancer risk as well as with survival time. However, prior studies, emphasizing particular subgroups, were relatively small. Therefore, we comprehensively evaluated ovarian and breast cancer risks as well as clinical outcome associated with rs61764370. Methods Centralized genotyping and analysis were performed for 140,012 women enrolled in the Ovarian Cancer Association Consortium (15,357 ovarian cancer patients; 30,816 controls), the Breast Cancer Association Consortium (33,530 breast cancer patients; 37,640 controls), and the Consortium of Modifiers of BRCA1 and BRCA2 (14,765 BRCA1 and 7904 BRCA2 mutation carriers). Results We found no association with risk of ovarian cancer (OR = 0.99, 95% CI 0.94-1.04, p = 0.74) or breast cancer (OR = 0.98, 95% CI 0.94-1.01, p = 0.19) and results were consistent among mutation carriers (BRCA1, ovarian cancer HR = 1.09, 95% CI 0.97-1.23, p = 0.14, breast cancer HR = 1.04, 95% CI 0.97-1.12, p = 0.27; BRCA2, ovarian cancer HR = 0.89, 95% CI 0.71-1.13, p = 0.34, breast cancer HR = 1.06, 95% CI 0.94-1.19, p = 0.35). Null results were also obtained for associations with overall survival following ovarian cancer (HR = 0.94, 95% CI 0.83-1.07, p = 0.38), breast cancer (HR = 0.96, 95% CI 0.87-1.06, p = 0.38), and all other previously-reported associations. Conclusions rs61764370 is not associated with risk of ovarian or breast cancer nor with clinical outcome for patients with these cancers. Therefore, genotyping this variant has no clinical utility related to the prediction or management of these cancers.
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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. |
- Chown, Ryan, et al.
(författare)
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PDRs4All: IV. An embarrassment of riches: Aromatic infrared bands in the Orion Bar
- 2024
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Ingår i: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 685
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Tidskriftsartikel (refereegranskat)abstract
- Context. Mid-infrared observations of photodissociation regions (PDRs) are dominated by strong emission features called aromatic infrared bands (AIBs). The most prominent AIBs are found at 3.3, 6.2, 7.7, 8.6, and 11.2 µm. The most sensitive, highest-resolution infrared spectral imaging data ever taken of the prototypical PDR, the Orion Bar, have been captured by JWST. These high-quality data allow for an unprecedentedly detailed view of AIBs. Aims. We provide an inventory of the AIBs found in the Orion Bar, along with mid-IR template spectra from five distinct regions in the Bar: the molecular PDR (i.e. the three H2 dissociation fronts), the atomic PDR, and the H II region. Methods. We used JWST NIRSpec IFU and MIRI MRS observations of the Orion Bar from the JWST Early Release Science Program, PDRs4All (ID: 1288). We extracted five template spectra to represent the morphology and environment of the Orion Bar PDR. We investigated and characterised the AIBs in these template spectra. We describe the variations among them here. Results. The superb sensitivity and the spectral and spatial resolution of these JWST observations reveal many details of the AIB emission and enable an improved characterization of their detailed profile shapes and sub-components. The Orion Bar spectra are dominated by the well-known AIBs at 3.3, 6.2, 7.7, 8.6, 11.2, and 12.7 µm with well-defined profiles. In addition, the spectra display a wealth of weaker features and sub-components. The widths of many AIBs show clear and systematic variations, being narrowest in the atomic PDR template, but showing a clear broadening in the H II region template while the broadest bands are found in the three dissociation front templates. In addition, the relative strengths of AIB (sub-)components vary among the template spectra as well. All AIB profiles are characteristic of class A sources as designated by Peeters (2022, A&A, 390, 1089), except for the 11.2 µm AIB profile deep in the molecular zone, which belongs to class B11.2. Furthermore, the observations show that the sub-components that contribute to the 5.75, 7.7, and 11.2 µm AIBs become much weaker in the PDR surface layers. We attribute this to the presence of small, more labile carriers in the deeper PDR layers that are photolysed away in the harsh radiation field near the surface. The 3.3/11.2 AIB intensity ratio decreases by about 40% between the dissociation fronts and the H II region, indicating a shift in the polycyclic aromatic hydrocarbon (PAH) size distribution to larger PAHs in the PDR surface layers, also likely due to the effects of photochemistry. The observed broadening of the bands in the molecular PDR is consistent with an enhanced importance of smaller PAHs since smaller PAHs attain a higher internal excitation energy at a fixed photon energy. Conclusions. Spectral-imaging observations of the Orion Bar using JWST yield key insights into the photochemical evolution of PAHs, such as the evolution responsible for the shift of 11.2 µm AIB emission from class B11.2 in the molecular PDR to class A11.2 in the PDR surface layers. This photochemical evolution is driven by the increased importance of FUV processing in the PDR surface layers, resulting in a “weeding out” of the weakest links of the PAH family in these layers. For now, these JWST observations are consistent with a model in which the underlying PAH family is composed of a few species: the so-called ‘grandPAHs’.
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| 5. |
- Habart, Emilie, et al.
(författare)
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PDRs4All II. JWST’s NIR and MIR imaging view of the Orion Nebula
- 2024
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Ingår i: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 685
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Tidskriftsartikel (refereegranskat)abstract
- Context. The James Webb Space Telescope (JWST) has captured the most detailed and sharpest infrared (IR) images ever taken of the inner region of the Orion Nebula, the nearest massive star formation region, and a prototypical highly irradiated dense photo-dissociation region (PDR). Aims. We investigate the fundamental interaction of far-ultraviolet (FUV) photons with molecular clouds. The transitions across the ionization front (IF), dissociation front (DF), and the molecular cloud are studied at high-angular resolution. These transitions are relevant to understanding the effects of radiative feedback from massive stars and the dominant physical and chemical processes that lead to the IR emission that JWST will detect in many Galactic and extragalactic environments. Methods. We utilized NIRCam and MIRI to obtain sub-arcsecond images over ∼150′′ and 42′′ in key gas phase lines (e.g., Pa α, Br α, [FeII] 1.64 µm, H2 1–0 S(1) 2.12 µm, 0–0 S(9) 4.69 µm), aromatic and aliphatic infrared bands (aromatic infrared bands at 3.3–3.4 µm, 7.7, and 11.3 µm), dust emission, and scattered light. Their emission are powerful tracers of the IF and DF, FUV radiation field and density distribution. Using NIRSpec observations the fractional contributions of lines, AIBs, and continuum emission to our NIRCam images were estimated. A very good agreement is found for the distribution and intensity of lines and AIBs between the NIRCam and NIRSpec observations. Results. Due to the proximity of the Orion Nebula and the unprecedented angular resolution of JWST, these data reveal that the molecular cloud borders are hyper structured at small angular scales of ∼0.1–1′′ (∼0.0002–0.002 pc or ∼40–400 au at 414 pc). A diverse set of features are observed such as ridges, waves, globules and photoevaporated protoplanetary disks. At the PDR atomic to molecular transition, several bright features are detected that are associated with the highly irradiated surroundings of the dense molecular condensations and embedded young star. Toward the Orion Bar PDR, a highly sculpted interface is detected with sharp edges and density increases near the IF and DF. This was predicted by previous modeling studies, but the fronts were unresolved in most tracers. The spatial distribution of the AIBs reveals that the PDR edge is steep and is followed by an extensive warm atomic layer up to the DF with multiple ridges. A complex, structured, and folded H0/H2 DF surface was traced by the H2 lines. This dataset was used to revisit the commonly adopted 2D PDR structure of the Orion Bar as our observations show that a 3D “terraced” geometry is required to explain the JWST observations. JWST provides us with a complete view of the PDR, all the way from the PDR edge to the substructured dense region, and this allowed us to determine, in detail, where the emission of the atomic and molecular lines, aromatic bands, and dust originate. Conclusions. This study offers an unprecedented dataset to benchmark and transform PDR physico-chemical and dynamical models for the JWST era. A fundamental step forward in our understanding of the interaction of FUV photons with molecular clouds and the role of FUV irradiation along the star formation sequence is provided.
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| 6. |
- Peeters, Els, et al.
(författare)
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PDRs4All: III. JWST's NIR spectroscopic view of the Orion Bar
- 2024
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Ingår i: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 685
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Tidskriftsartikel (refereegranskat)abstract
- Context. JWST has taken the sharpest and most sensitive infrared (IR) spectral imaging observations ever of the Orion Bar photodis-sociation region (PDR), which is part of the nearest massive star-forming region the Orion Nebula, and often considered to be the 'prototypical'strongly illuminated PDR. Aims. We investigate the impact of radiative feedback from massive stars on their natal cloud and focus on the transition from the H II region to the atomic PDR -crossing the ionisation front (IF) -, and the subsequent transition to the molecular PDR -crossing the dissociation front (DF). Given the prevalence of PDRs in the interstellar medium and their dominant contribution to IR radiation, understanding the response of the PDR gas to far-ultraviolet (FUV) photons and the associated physical and chemical processes is fundamental to our understanding of star and planet formation and for the interpretation of any unresolved PDR as seen by JWST. Methods. We used high-resolution near-IR integral field spectroscopic data from NIRSpec on JWST to observe the Orion Bar PDR as part of the PDRs4All JWST Early Release Science programme. We constructed a 3″ × 25″ spatio-spectral mosaic covering 0.97-5.27 μm at a spectral resolution R of ~2700 and an angular resolution of 0.075″-0.173″. To study the properties of key regions captured in this mosaic, we extracted five template spectra in apertures centred on the three H2 dissociation fronts, the atomic PDR, and the H II region. This wealth of detailed spatial-spectral information was analysed in terms of variations in the physical conditions-incident UV field, density, and temperature -of the PDR gas. Results. The NIRSpec data reveal a forest of lines including, but not limited to, He I, H I, and C I recombination lines; ionic lines (e.g. Fe III and Fe II); O I and N I fluorescence lines; aromatic infrared bands (AIBs, including aromatic CH, aliphatic CH, and their CD counterparts); pure rotational and ro-vibrational lines from H2; and ro-vibrational lines from HD, CO, and CH+, with most of them having been detected for the first time towards a PDR. Their spatial distribution resolves the H and He ionisation structure in the Huygens region, gives insight into the geometry of the Bar, and confirms the large-scale stratification of PDRs. In addition, we observed numerous smaller-scale structures whose typical size decreases with distance from θ1 Ori C and IR lines from C I, if solely arising from radiative recombination and cascade, reveal very high gas temperatures (a few 1000 K) consistent with the hot irradiated surface of small-scale dense clumps inside the PDR. The morphology of the Bar, in particular that of the H2 lines, reveals multiple prominent filaments that exhibit different characteristics. This leaves the impression of a 'terraced'transition from the predominantly atomic surface region to the CO-rich molecular zone deeper in. We attribute the different characteristics of the H2 filaments to their varying depth into the PDR and, in some cases, not reaching the C+/C/CO transition. These observations thus reveal what local conditions are required to drive the physical and chemical processes needed to explain the different characteristics of the DFs and the photochemical evolution of the AIB carriers. Conclusions. This study showcases the discovery space created by JWST to further our understanding of the impact radiation from young stars has on their natal molecular cloud and proto-planetary disk, which touches on star and planet formation as well as galaxy evolution.
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| 7. |
- Feng, Shaohong, et al.
(författare)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 8. |
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| 9. |
- Berne, Olivier, et al.
(författare)
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PDRs4All : A JWST Early Release Science Program on Radiative Feedback from Massive Stars
- 2022
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Ingår i: Publications of the Astronomical Society of the Pacific. - : IOP Publishing. - 0004-6280 .- 1538-3873. ; 134:1035
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Tidskriftsartikel (refereegranskat)abstract
- Massive stars disrupt their natal molecular cloud material through radiative and mechanical feedback processes. These processes have profound effects on the evolution of interstellar matter in our Galaxy and throughout the universe, from the era of vigorous star formation at redshifts of 1-3 to the present day. The dominant feedback processes can be probed by observations of the Photo-Dissociation Regions (PDRs) where the far-ultraviolet photons of massive stars create warm regions of gas and dust in the neutral atomic and molecular gas. PDR emission provides a unique tool to study in detail the physical and chemical processes that are relevant for most of the mass in inter- and circumstellar media including diffuse clouds, proto-planetary disks, and molecular cloud surfaces, globules, planetary nebulae, and star-forming regions. PDR emission dominates the infrared (IR) spectra of star-forming galaxies. Most of the Galactic and extragalactic observations obtained with the James Webb Space Telescope (JWST) will therefore arise in PDR emission. In this paper we present an Early Release Science program using the MIRI, NIRSpec, and NIRCam instruments dedicated to the observations of an emblematic and nearby PDR: the Orion Bar. These early JWST observations will provide template data sets designed to identify key PDR characteristics in JWST observations. These data will serve to benchmark PDR models and extend them into the JWST era. We also present the Science-Enabling products that we will provide to the community. These template data sets and Science-Enabling products will guide the preparation of future proposals on star-forming regions in our Galaxy and beyond and will facilitate data analysis and interpretation of forthcoming JWST observations.
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| 10. |
- Olefeldt, David, et al.
(författare)
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The Boreal-Arctic Wetland and Lake Dataset (BAWLD)
- 2021
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Ingår i: Earth System Science Data. - : Copernicus Gesellschaft MBH. - 1866-3508 .- 1866-3516. ; 13:11, s. 5127-5149
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Tidskriftsartikel (refereegranskat)abstract
- Methane emissions from boreal and arctic wetlands, lakes, and rivers are expected to increase in response to warming and associated permafrost thaw. However, the lack of appropriate land cover datasets for scaling field-measured methane emissions to circumpolar scales has contributed to a large uncertainty for our understanding of present-day and future methane emissions. Here we present the BorealArctic Wetland and Lake Dataset (BAWLD), a land cover dataset based on an expert assessment, extrapolated using random forest modelling from available spatial datasets of climate, topography, soils, permafrost conditions, vegetation, wetlands, and surface water extents and dynamics. In BAWLD, we estimate the fractional coverage of five wetland, seven lake, and three river classes within 0.5 x 0.5 degrees grid cells that cover the northern boreal and tundra biomes (17 % of the global land surface). Land cover classes were defined using criteria that ensured distinct methane emissions among classes, as indicated by a co-developed comprehensive dataset of methane flux observations. In BAWLD, wetlands occupied 3.2 x 10(6) km(2) (14 % of domain) with a 95 % confidence interval between 2.8 and 3.8 x 10(6) km(2). Bog, fen, and permafrost bog were the most abundant wetland classes, covering similar to 28 % each of the total wetland area, while the highest-methane-emitting marsh and tundra wetland classes occupied 5 % and 12 %, respectively. Lakes, defined to include all lentic open-water ecosystems regardless of size, covered 1.4 x 10(6) km(2) (6 % of domain). Low-methane-emitting large lakes (>10 km(2)) and glacial lakes jointly represented 78 % of the total lake area, while high-emitting peatland and yedoma lakes covered 18 % and 4 %, respectively. Small (<0.1 km(2)) glacial, peatland, and yedoma lakes combined covered 17 % of the total lake area but contributed disproportionally to the overall spatial uncertainty in lake area with a 95 % confidence interval between 0.15 and 0.38 x 10(6) km(2). Rivers and streams were estimated to cover 0.12 x 10(6) km(2) (0.5 % of domain), of which 8 % was associated with high-methane-emitting headwaters that drain organic-rich landscapes. Distinct combinations of spatially co-occurring wetland and lake classes were identified across the BAWLD domain, allowing for the mapping of "wetscapes" that have characteristic methane emission magnitudes and sensitivities to climate change at regional scales. With BAWLD, we provide a dataset which avoids double-accounting of wetland, lake, and river extents and which includes confidence intervals for each land cover class. As such, BAWLD will be suitable for many hydrological and biogeochemical modelling and upscaling efforts for the northern boreal and arctic region, in particular those aimed at improving assessments of current and future methane emissions.
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| 11. |
- Abbott, Benjamin W., et al.
(författare)
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Biomass offsets little or none of permafrost carbon release from soils, streams, and wildfire : an expert assessment
- 2016
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Ingår i: Environmental Research Letters. - : IOP Publishing. - 1748-9326. ; 11:3
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Tidskriftsartikel (refereegranskat)abstract
- As the permafrost region warms, its large organic carbon pool will be increasingly vulnerable to decomposition, combustion, and hydrologic export. Models predict that some portion of this release will be offset by increased production of Arctic and boreal biomass; however, the lack of robust estimates of net carbon balance increases the risk of further overshooting international emissions targets. Precise empirical or model-based assessments of the critical factors driving carbon balance are unlikely in the near future, so to address this gap, we present estimates from 98 permafrost-region experts of the response of biomass, wildfire, and hydrologic carbon flux to climate change. Results suggest that contrary to model projections, total permafrost-region biomass could decrease due to water stress and disturbance, factors that are not adequately incorporated in current models. Assessments indicate that end-of-the-century organic carbon release from Arctic rivers and collapsing coastlines could increase by 75% while carbon loss via burning could increase four-fold. Experts identified water balance, shifts in vegetation community, and permafrost degradation as the key sources of uncertainty in predicting future system response. In combination with previous findings, results suggest the permafrost region will become a carbon source to the atmosphere by 2100 regardless of warming scenario but that 65%-85% of permafrost carbon release can still be avoided if human emissions are actively reduced.
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| 12. |
- Post, Eric, et al.
(författare)
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Ecological Dynamics Across the Arctic Associated with Recent Climate Change
- 2009
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 325:5946, s. 1355-1358
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Forskningsöversikt (refereegranskat)abstract
- At the close of the Fourth International Polar Year, we take stock of the ecological consequences of recent climate change in the Arctic, focusing on effects at population, community, and ecosystem scales. Despite the buffering effect of landscape heterogeneity, Arctic ecosystems and the trophic relationships that structure them have been severely perturbed. These rapid changes may be a bellwether of changes to come at lower latitudes and have the potential to affect ecosystem services related to natural resources, food production, climate regulation, and cultural integrity. We highlight areas of ecological research that deserve priority as the Arctic continues to warm.
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| 13. |
- Turetsky, Merritt R., et al.
(författare)
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Carbon release through abrupt permafrost thaw
- 2020
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Ingår i: Nature Geoscience. - : Springer Science and Business Media LLC. - 1752-0894 .- 1752-0908. ; 13:2, s. 138-
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Tidskriftsartikel (refereegranskat)abstract
- The permafrost zone is expected to be a substantial carbon source to the atmosphere, yet large-scale models currently only simulate gradual changes in seasonally thawed soil. Abrupt thaw will probably occur in <20% of the permafrost zone but could affect half of permafrost carbon through collapsing ground, rapid erosion and landslides. Here, we synthesize the best available information and develop inventory models to simulate abrupt thaw impacts on permafrost carbon balance. Emissions across 2.5 million km(2) of abrupt thaw could provide a similar climate feedback as gradual thaw emissions from the entire 18 million km(2) permafrost region under the warming projection of Representative Concentration Pathway 8.5. While models forecast that gradual thaw may lead to net ecosystem carbon uptake under projections of Representative Concentration Pathway 4.5, abrupt thaw emissions are likely to offset this potential carbon sink. Active hillslope erosional features will occupy 3% of abrupt thaw terrain by 2300 but emit one-third of abrupt thaw carbon losses. Thaw lakes and wetlands are methane hot spots but their carbon release is partially offset by slowly regrowing vegetation. After considering abrupt thaw stabilization, lake drainage and soil carbon uptake by vegetation regrowth, we conclude that models considering only gradual permafrost thaw are substantially underestimating carbon emissions from thawing permafrost.
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| 14. |
- McGuire, A. David, et al.
(författare)
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Variability in the sensitivity among model simulations of permafrost and carbon dynamics in the permafrost region between 1960 and 2009
- 2016
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Ingår i: Global Biogeochemical Cycles. - 0886-6236 .- 1944-9224. ; 30:7, s. 1015-1037
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Tidskriftsartikel (refereegranskat)abstract
- A significant portion of the large amount of carbon (C) currently stored in soils of the permafrost region in the Northern Hemisphere has the potential to be emitted as the greenhouse gases CO2 and CH4 under a warmer climate. In this study we evaluated the variability in the sensitivity of permafrost and C in recent decades among land surface model simulations over the permafrost region between 1960 and 2009. The 15 model simulations all predict a loss of near-surface permafrost (within 3m) area over the region, but there are large differences in the magnitude of the simulated rates of loss among the models (0.2 to 58.8x10(3)km(2)yr(-1)). Sensitivity simulations indicated that changes in air temperature largely explained changes in permafrost area, although interactions among changes in other environmental variables also played a role. All of the models indicate that both vegetation and soil C storage together have increased by 156 to 954TgCyr(-1) between 1960 and 2009 over the permafrost region even though model analyses indicate that warming alone would decrease soil C storage. Increases in gross primary production (GPP) largely explain the simulated increases in vegetation and soil C. The sensitivity of GPP to increases in atmospheric CO2 was the dominant cause of increases in GPP across the models, but comparison of simulated GPP trends across the 1982-2009 period with that of a global GPP data set indicates that all of the models overestimate the trend in GPP. Disturbance also appears to be an important factor affecting C storage, as models that consider disturbance had lower increases in C storage than models that did not consider disturbance. To improve the modeling of C in the permafrost region, there is the need for the modeling community to standardize structural representation of permafrost and carbon dynamics among models that are used to evaluate the permafrost C feedback and for the modeling and observational communities to jointly develop data sets and methodologies to more effectively benchmark models.
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| 15. |
- Ramirez, Kelly S., et al.
(författare)
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Detecting macroecological patterns in bacterial communities across independent studies of global soils
- 2018
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Ingår i: Nature Microbiology. - : NATURE PUBLISHING GROUP. - 2058-5276. ; 3:2, s. 189-196
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Tidskriftsartikel (refereegranskat)abstract
- The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential 'indicator' taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.
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| 16. |
- Harden, Jennifer W., et al.
(författare)
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Field information links permafrost carbon to physical vulnerabilities of thawing
- 2012
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Ingår i: Geophysical Research Letters. - 0094-8276 .- 1944-8007. ; 39, s. L15704-
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Tidskriftsartikel (refereegranskat)abstract
- Deep soil profiles containing permafrost (Gelisols) were characterized for organic carbon (C) and total nitrogen (N) stocks to 3 m depths. Using the Community Climate System Model (CCSM4) we calculate cumulative distributions of active layer thickness (ALT) under current and future climates. The difference in cumulative ALT distributions over time was multiplied by C and N contents of soil horizons in Gelisol suborders to calculate newly thawed C and N. Thawing ranged from 147 PgC with 10 PgN by 2050 (representative concentration pathway RCP scenario 4.5) to 436 PgC with 29 PgN by 2100 (RCP 8.5). Organic horizons that thaw are vulnerable to combustion, and all horizon types are vulnerable to shifts in hydrology and decomposition. The rates and extent of such losses are unknown and can be further constrained by linking field and modelling approaches. These changes have the potential for strong additional loading to our atmosphere, water resources, and ecosystems. Citation: Harden, J. W., et al. (2012), Field information links permafrost carbon to physical vulnerabilities of thawing, Geophys. Res. Lett., 39, L15704, doi: 10.1029/2012GL051958.
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| 17. |
- Luo, Yiqi, et al.
(författare)
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Toward more realistic projections of soil carbon dynamics by Earth system models
- 2016
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Ingår i: Global Biogeochemical Cycles. - 0886-6236. ; 30:1, s. 40-56
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Tidskriftsartikel (refereegranskat)abstract
- Soil carbon (C) is a critical component of Earth system models (ESMs), and its diverse representations are a major source of the large spread across models in the terrestrial C sink from the third to fifth assessment reports of the Intergovernmental Panel on Climate Change (IPCC). Improving soil C projections is of a high priority for Earth system modeling in the future IPCC and other assessments. To achieve this goal, we suggest that (1) model structures should reflect real-world processes, (2) parameters should be calibrated to match model outputs with observations, and (3) external forcing variables should accurately prescribe the environmental conditions that soils experience. First, most soil C cycle models simulate C input from litter production and C release through decomposition. The latter process has traditionally been represented by first-order decay functions, regulated primarily by temperature, moisture, litter quality, and soil texture. While this formulation well captures macroscopic soil organic C (SOC) dynamics, better understanding is needed of their underlying mechanisms as related to microbial processes, depth-dependent environmental controls, and other processes that strongly affect soil C dynamics. Second, incomplete use of observations in model parameterization is a major cause of bias in soil C projections from ESMs. Optimal parameter calibration with both pool- and flux-based data sets through data assimilation is among the highest priorities for near-term research to reduce biases among ESMs. Third, external variables are represented inconsistently among ESMs, leading to differences in modeled soil C dynamics. We recommend the implementation of traceability analyses to identify how external variables and model parameterizations influence SOC dynamics in different ESMs. Overall, projections of the terrestrial C sink can be substantially improved when reliable data sets are available to select the most representative model structure, constrain parameters, and prescribe forcing fields.
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| 18. |
- Wang, Wenli, et al.
(författare)
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Evaluation of air-soil temperature relationships simulated by land surface models during winter across the permafrost region
- 2016
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Ingår i: Cryosphere. - : Copernicus GmbH. - 1994-0416. ; 10:4, s. 1721-1737
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Tidskriftsartikel (refereegranskat)abstract
- A realistic simulation of snow cover and its thermal properties are important for accurate modelling of permafrost. We analyse simulated relationships between air and near-surface (20 cm) soil temperatures in the Northern Hemisphere permafrost region during winter, with a particular focus on snow insulation effects in nine land surface models, and compare them with observations from 268 Russian stations. There are large cross-model differences in the simulated differences between near-surface soil and air temperatures (ΔT; 3 to 14 °C), in the sensitivity of soil-to-air temperature (0.13 to 0.96 °C °C-1), and in the relationship between ΔT and snow depth. The observed relationship between ΔT and snow depth can be used as a metric to evaluate the effects of each model's representation of snow insulation, hence guide improvements to the model's conceptual structure and process parameterisations. Models with better performance apply multilayer snow schemes and consider complex snow processes. Some models show poor performance in representing snow insulation due to underestimation of snow depth and/or overestimation of snow conductivity. Generally, models identified as most acceptable with respect to snow insulation simulate reasonable areas of near-surface permafrost (13.19 to 15.77 million km2). However, there is not a simple relationship between the sophistication of the snow insulation in the acceptable models and the simulated area of Northern Hemisphere near-surface permafrost, because several other factors, such as soil depth used in the models, the treatment of soil organic matter content, hydrology and vegetation cover, also affect the simulated permafrost distribution.
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| 19. |
- Xia, Jianyang, et al.
(författare)
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Terrestrial ecosystem model performance in simulating productivity and its vulnerability to climate change in the northern permafrost region
- 2017
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Ingår i: Journal of Geophysical Research - Biogeosciences. - 2169-8953. ; 122:2, s. 430-446
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Tidskriftsartikel (refereegranskat)abstract
- Realistic projection of future climate-carbon (C) cycle feedbacks requires better understanding and an improved representation of the C cycle in permafrost regions in the current generation of Earth system models. Here we evaluated 10 terrestrial ecosystem models for their estimates of net primary productivity (NPP) and responses to historical climate change in permafrost regions in the Northern Hemisphere. In comparison with the satellite estimate from the Moderate Resolution Imaging Spectroradiometer (MODIS; 246±6gCm-2yr-1), most models produced higher NPP (309±12gCm-2yr-1) over the permafrost region during 2000-2009. By comparing the simulated gross primary productivity (GPP) with a flux tower-based database, we found that although mean GPP among the models was only overestimated by 10% over 1982-2009, there was a twofold discrepancy among models (380 to 800gCm-2yr-1), which mainly resulted from differences in simulated maximum monthly GPP (GPPmax). Most models overestimated C use efficiency (CUE) as compared to observations at both regional and site levels. Further analysis shows that model variability of GPP and CUE are nonlinearly correlated to variability in specific leaf area and the maximum rate of carboxylation by the enzyme Rubisco at 25°C (Vcmax_25), respectively. The models also varied in their sensitivities of NPP, GPP, and CUE to historical changes in climate and atmospheric CO2 concentration. These results indicate that model predictive ability of the C cycle in permafrost regions can be improved by better representation of the processes controlling CUE and GPPmax as well as their sensitivity to climate change.
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| 20. |
- Andresen, Christian G., et al.
(författare)
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Soil moisture and hydrology projections of the permafrost region-a model intercomparison
- 2020
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Ingår i: Cryosphere. - : Copernicus GmbH. - 1994-0416. ; 14:2, s. 445-459
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Tidskriftsartikel (refereegranskat)abstract
- This study investigates and compares soil moisture and hydrology projections of broadly used land models with permafrost processes and highlights the causes and impacts of permafrost zone soil moisture projections. Climate models project warmer temperatures and increases in precipitation (P) which will intensify evapotranspiration (ET) and runoff in land models. However, this study shows that most models project a long-term drying of the surface soil (0-20 cm) for the permafrost region despite increases in the net air-surface water flux (P-ET). Drying is generally explained by infiltration of moisture to deeper soil layers as the active layer deepens or permafrost thaws completely. Although most models agree on drying, the projections vary strongly in magnitude and spatial pattern. Land models tend to agree with decadal runoff trends but underestimate runoff volume when compared to gauge data across the major Arctic river basins, potentially indicating model structural limitations. Coordinated efforts to address the ongoing challenges presented in this study will help reduce uncertainty in our capability to predict the future Arctic hydrological state and associated land-atmosphere biogeochemical processes across spatial and temporal scales.
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| 21. |
- Kuhn, McKenzie A., et al.
(författare)
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BAWLD-CH4 : a comprehensive dataset of methane fluxes from boreal and arctic ecosystems
- 2021
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Ingår i: Earth System Science Data. - : Copernicus Gesellschaft MBH. - 1866-3508 .- 1866-3516. ; 13:11, s. 5151-5189
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Tidskriftsartikel (refereegranskat)abstract
- Methane (CH4) emissions from the boreal and arctic region are globally significant and highly sensitive to climate change. There is currently a wide range in estimates of high-latitude annual CH4 fluxes, where estimates based on land cover inventories and empirical CH4 flux data or process models (bottom-up approaches) generally are greater than atmospheric inversions (top-down approaches). A limitation of bottom-up approaches has been the lack of harmonization between inventories of site-level CH4 flux data and the land cover classes present in high-latitude spatial datasets. Here we present a comprehensive dataset of small-scale, surface CH4 flux data from 540 terrestrial sites (wetland and non-wetland) and 1247 aquatic sites (lakes and ponds), compiled from 189 studies. The Boreal-Arctic Wetland and Lake Methane Dataset (BAWLD-CH4) was constructed in parallel with a compatible land cover dataset, sharing the same land cover classes to enable refined bottom-up assessments. BAWLD-CH4 includes information on site-level CH4 fluxes but also on study design (measurement method, timing, and frequency) and site characteristics (vegetation, climate, hydrology, soil, and sediment types, permafrost conditions, lake size and depth, and our determination of land cover class). The different land cover classes had distinct CH4 fluxes, resulting from definitions that were either based on or co-varied with key environmental controls. Fluxes of CH4 from terrestrial ecosystems were primarily influenced by water table position, soil temperature, and vegetation composition, while CH4 fluxes from aquatic ecosystems were primarily influenced by water temperature, lake size, and lake genesis. Models could explain more of the between-site variability in CH4 fluxes for terrestrial than aquatic ecosystems, likely due to both less precise assessments of lake CH4 fluxes and fewer consistently reported lake site characteristics. Analysis of BAWLD-CH4 identified both land cover classes and regions within the boreal and arctic domain, where future studies should be focused, alongside methodological approaches. Overall, BAWLD-CH4 provides a comprehensive dataset of CH4 emissions from high-latitude ecosystems that are useful for identifying research opportunities, for comparison against new field data, and model parameterization or validation.
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| 22. |
- McGuire, A. David, et al.
(författare)
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The carbon budget of the northern cryosphere region
- 2010
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Ingår i: Current Opinion in Environmental Sustainability. - : Elsevier BV. - 1877-3435 .- 1877-3443. ; 2:4, s. 231-236
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Forskningsöversikt (refereegranskat)abstract
- The northern cryosphere is undergoing substantial warming of permafrost and loss of sea ice. Release of stored carbon to the atmosphere in response to this change has the potential to affect the global climate system. Studies indicate that the northern cryosphere has been not only a substantial sink for atmospheric CO2 in recent decades, but also an important source of CH4 because of emissions from wetlands and lakes. Analyses suggest that the sensitivity of the carbon cycle of the region over the 21st Century is potentially large, but highly uncertain because numerous pathways of response will be affected by warming. Further research should focus on sensitive elements of the carbon cycle such as the consequences of increased fire disturbance, permafrost degradation, and sea ice loss in the northern cryosphere region.
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| 23. |
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| 24. |
- Olefeldt, David, et al.
(författare)
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Environmental and physical controls on northern terrestrial methane emissions across permafrost zones
- 2013
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Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 19:2, s. 589-603
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Tidskriftsartikel (refereegranskat)abstract
- Methane (CH4) emissions from the northern high-latitude region represent potentially significant biogeochemical feedbacks to the climate system. We compiled a database of growing-season CH4 emissions from terrestrial ecosystems located across permafrost zones, including 303 sites described in 65 studies. Data on environmental and physical variables, including permafrost conditions, were used to assess controls on CH4 emissions. Water table position, soil temperature, and vegetation composition strongly influenced emissions and had interacting effects. Sites with a dense sedge cover had higher emissions than other sites at comparable water table positions, and this was an effect that was more pronounced at low soil temperatures. Sensitivity analysis suggested that CH4 emissions from ecosystems where the water table on average is at or above the soil surface (wet tundra, fen underlain by permafrost, and littoral ecosystems) are more sensitive to variability in soil temperature than drier ecosystems (palsa dry tundra, bog, and fen), whereas the latter ecosystems conversely are relatively more sensitive to changes of the water table position. Sites with near-surface permafrost had lower CH4 fluxes than sites without permafrost at comparable water table positions, a difference that was explained by lower soil temperatures. Neither the active layer depth nor the organic soil layer depth was related to CH4 emissions. Permafrost thaw in lowland regions is often associated with increased soil moisture, higher soil temperatures, and increased sedge cover. In our database, lowland thermokarst sites generally had higher emissions than adjacent sites with intact permafrost, but emissions from thermokarst sites were not statistically higher than emissions from permafrost-free sites with comparable environmental conditions. Overall, these results suggest that future changes to terrestrial high-latitude CH4 emissions will be more proximately related to changes in moisture, soil temperature, and vegetation composition than to increased availability of organic matter following permafrost thaw.
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| 25. |
- Parmentier, Frans-Jan, et al.
(författare)
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The impact of lower sea-ice extent on Arctic greenhouse-gas exchange
- 2013
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Ingår i: Nature Climate Change. - 1758-6798. ; 3:3, s. 195-202
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Tidskriftsartikel (refereegranskat)abstract
- In September 2012, Arctic sea-ice extent plummeted to a new record low: two times lower than the 1979-2000 average. Often, record lows in sea-ice cover are hailed as an example of climate change impacts in the Arctic. Less apparent, however, are the implications of reduced sea-ice cover in the Arctic Ocean for marine-atmosphere CO2 exchange. Sea-ice decline has been connected to increasing air temperatures at high latitudes. Temperature is a key controlling factor in the terrestrial exchange of CO2 and methane, and therefore the greenhouse-gas balance of the Arctic. Despite the large potential for feedbacks, many studies do not connect the diminishing sea-ice extent with changes in the interaction of the marine and terrestrial Arctic with the atmosphere. In this Review, we assess how current understanding of the Arctic Ocean and high-latitude ecosystems can be used to predict the impact of a lower sea-ice cover on Arctic greenhouse-gas exchange.
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| 26. |
- Sayedi, Sayedeh Sara, et al.
(författare)
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Subsea permafrost carbon stocks and climate change sensitivity estimated by expert assessment
- 2020
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Ingår i: Environmental Research Letters. - : IOP Publishing. - 1748-9326. ; 15:12
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Tidskriftsartikel (refereegranskat)abstract
- The continental shelves of the Arctic Ocean and surrounding seas contain large stocks of organic matter (OM) and methane (CH4), representing a potential ecosystem feedback to climate change not included in international climate agreements. We performed a structured expert assessment with 25 permafrost researchers to combine quantitative estimates of the stocks and sensitivity of organic carbon in the subsea permafrost domain (i.e. unglaciated portions of the continental shelves exposed during the last glacial period). Experts estimated that the subsea permafrost domain contains similar to 560 gigatons carbon (GtC; 170-740, 90% confidence interval) in OM and 45 GtC (10-110) in CH4. Current fluxes of CH4 and carbon dioxide (CO2) to the water column were estimated at 18 (2-34) and 38 (13-110) megatons C yr(-1), respectively. Under Representative Concentration Pathway (RCP) RCP8.5, the subsea permafrost domain could release 43 Gt CO2-equivalent (CO(2)e) by 2100 (14-110) and 190 Gt CO(2)e by 2300 (45-590), with similar to 30% fewer emissions under RCP2.6. The range of uncertainty demonstrates a serious knowledge gap but provides initial estimates of the magnitude and timing of the subsea permafrost climate feedback.
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| 27. |
- James, Stefan, 1964-, et al.
(författare)
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Rationale and design of the DAPA-MI trial : Dapagliflozin in patients without diabetes mellitus with acute myocardial infarction
- 2023
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Ingår i: American Heart Journal. - : Elsevier. - 0002-8703 .- 1097-6744. ; 266, s. 188-197
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Tidskriftsartikel (refereegranskat)abstract
- Background Therapies that could further prevent the development of heart failure (HF) and other cardiovascular and metabolic events in patients with recent myocardial infarction (MI) represent a large and unmet medical need. Methods DAPA-MI is a multicenter, parallel-group, registry-based, randomized, double-blind, placebo-controlled phase 3 trial in patients without known diabetes or established HF, presenting with MI and impaired left ventricular systolic function or Q-wave MI. The trial evaluated the effect of dapagliflozin 10 mg vs placebo, given once daily in addition to standard of care therapy, on death, hospitalization for HF (HHF), and other cardiometabolic outcomes. The primary objective of the trial was to determine, using the win-ratio method, if dapagliflozin is superior to placebo by comparing the hierarchical composite outcome of death, HHF, nonfatal MI, atrial fibrillation/flutter, new onset of type 2 diabetes mellitus, HF symptoms as measured by New York Heart Association Functional Classification at last visit, and body weight decrease >= 5% at last visit. Assuming a true win-ratio of 1.20 between dapagliflozin and placebo, 4,000 patients provide a statistical power of 80% for the test of the primary composite outcome. A registry-based randomized controlled trial framework allowed for recruitment, randomization, blinding, and pragmatic data collection of baseline demographics, medications, and clinical outcomes using existing national clinical registries (in Sweden and the UK) integrated with the trial database. Conclusions The trial explores opportunities to improve further the outcome of patients with impaired LV function after MI. The innovative trial design of DAPA-MI, incorporating national clinical registry data, has facilitated efficient patient recruitment as well as outcome ascertainment.
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| 28. |
- Li, Zhao, et al.
(författare)
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Non-uniform seasonal warming regulates vegetation greening and atmospheric CO2 amplification over northern lands
- 2018
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Ingår i: Environmental Research Letters. - : IOP Publishing. - 1748-9326. ; 13:12
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Tidskriftsartikel (refereegranskat)abstract
- The enhanced vegetation growth by climate warming plays a pivotal role in amplifying the seasonal cycle of atmospheric CO2 at northern lands (>50° N) since 1960s. However, the correlation between vegetation growth, temperature and seasonal amplitude of atmospheric CO2 concentration have become elusive with the slowed increasing trend of vegetation growth and weakened temperature control on CO2 uptake since late 1990s. Here, based on in situ atmospheric CO2 concentration records from the Barrow observatory site, we found a slowdown in the increasing trend of the atmospheric CO2 amplitude from 1990s to mid-2000s. This phenomenon was associated with the paused decrease in the minimum CO2 concentration ([CO2]min), which was significantly correlated with the slowdown of vegetation greening and growing-season length extension. We then showed that both the vegetation greenness and growing-season length were positively correlated with spring but not autumn temperature over the northern lands. Furthermore, such asymmetric dependences of vegetation growth upon spring and autumn temperature cannot be captured by the state-of-art terrestrial biosphere models. These findings indicate that the responses of vegetation growth to spring and autumn warming are asymmetric, and highlight the need of improving autumn phenology in the models for predicting seasonal cycle of atmospheric CO2 concentration.
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| 29. |
- Parmentier, Frans-Jan, et al.
(författare)
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Rising methane emissions from northern wetlands associated with sea ice decline
- 2015
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Ingår i: Geophysical Research Letters. - 1944-8007. ; 42:17, s. 7214-7222
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Tidskriftsartikel (refereegranskat)abstract
- The Arctic is rapidly transitioning toward a seasonal sea ice-free state, perhaps one of the most apparent examples of climate change in the world. This dramatic change has numerous consequences, including a large increase in air temperatures, which in turn may affect terrestrial methane emissions. Nonetheless, terrestrial and marine environments are seldom jointly analyzed. By comparing satellite observations of Arctic sea ice concentrations to methane emissions simulated by three process-based biogeochemical models, this study shows that rising wetland methane emissions are associated with sea ice retreat. Our analyses indicate that simulated high-latitude emissions for 2005-2010 were, on average, 1.7 Tg CH4 yr(-1) higher compared to 1981-1990 due to a sea ice-induced, autumn-focused, warming. Since these results suggest a continued rise in methane emissions with future sea ice decline, observation programs need to include measurements during the autumn to further investigate the impact of this spatial connection on terrestrial methane emissions.
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| 30. |
- Sitch, Stephen, et al.
(författare)
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Assessing the carbon balance of circumpolar Arctic tundra using remote sensing and process modeling
- 2007
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Ingår i: Ecological Applications. - : John Wiley & Sons. - 1051-0761 .- 1939-5582. ; 17:1, s. 213-234
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Tidskriftsartikel (refereegranskat)abstract
- This paper reviews the current status of using remote sensing and process-based modeling approaches to assess the contemporary and future circumpolar carbon balance of Arctic tundra, including the exchange of both carbon dioxide and methane with the atmosphere. Analyses based on remote sensing approaches that use a 20-year data record of satellite data indicate that tundra is greening in the Arctic, suggesting an increase in photosynthetic activity and net primary production. Modeling studies generally simulate a small net carbon sink for the distribution of Arctic tundra, a result that is within the uncertainty range of field-based estimates of net carbon exchange. Applications of processbased approaches for scenarios of future climate change generally indicate net carbon sequestration in Arctic tundra as enhanced vegetation production exceeds simulated increases in decomposition. However, methane emissions are likely to increase dramatically, in response to rising soil temperatures, over the next century. Key uncertainties in the response of Arctic ecosystems to climate change include uncertainties in future fire regimes and uncertainties relating to changes in the soil environment. These include the response of soil decomposition and respiration to warming and deepening of the soil active layer, uncertainties in precipitation and potential soil drying, and distribution of wetlands. While there are numerous uncertainties in the projections of process-based models, they generally indicate that Arctic tundra will be a small sink for carbon over the next century and that methane emissions will increase considerably, which implies that exchange of greenhouse gases between the atmosphere and Arctic tundra ecosystems is likely to contribute to climate warming.
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