| 1. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 2. |
- Alexander, Stephen P. H., et al.
(författare)
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The Concise Guide to PHARMACOLOGY 2023/24: G protein-coupled receptors
- 2023
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Ingår i: BRITISH JOURNAL OF PHARMACOLOGY. - : British pharmacological society. - 0007-1188 .- 1476-5381. ; 180
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Tidskriftsartikel (refereegranskat)abstract
- The Concise Guide to PHARMACOLOGY 2023/24 is the sixth in this series of biennial publications. The Concise Guide provides concise overviews, mostly in tabular format, of the key properties of approximately 1800 drug targets, and about 6000 interactions with about 3900 ligands. There is an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (), which provides more detailed views of target and ligand properties. Although the Concise Guide constitutes almost 500 pages, the material presented is substantially reduced compared to information and links presented on the website. It provides a permanent, citable, point-in-time record that will survive database updates. The full contents of this section can be found at . G protein-coupled receptors are one of the six major pharmacological targets into which the Guide is divided, with the others being: ion channels, nuclear hormone receptors, catalytic receptors, enzymes and transporters. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading. The landscape format of the Concise Guide is designed to facilitate comparison of related targets from material contemporary to mid-2023, and supersedes data presented in the 2021/22, 2019/20, 2017/18, 2015/16 and 2013/14 Concise Guides and previous Guides to Receptors and Channels. It is produced in close conjunction with the Nomenclature and Standards Committee of the International Union of Basic and Clinical Pharmacology (NC-IUPHAR), therefore, providing official IUPHAR classification and nomenclature for human drug targets, where appropriate.
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| 3. |
- Christopoulos, Arthur, et al.
(författare)
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THE CONCISE GUIDE TO PHARMACOLOGY 2021/22: G protein-coupled receptors.
- 2021
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Ingår i: British journal of pharmacology. - : Wiley. - 1476-5381 .- 0007-1188. ; 178 Suppl 1
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Forskningsöversikt (refereegranskat)abstract
- The Concise Guide to PHARMACOLOGY 2021/22 is the fifth in this series of biennial publications. The Concise Guide provides concise overviews, mostly in tabular format, of the key properties of nearly 1900 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties. Although the Concise Guide constitutes over 500 pages, the material presented is substantially reduced compared to information and links presented on the website. It provides a permanent, citable, point-in-time record that will survive database updates. The full contents of this section can be found at http://onlinelibrary.wiley.com/doi/bph.15538. G protein-coupled receptors are one of the six major pharmacological targets into which the Guide is divided, with the others being: ion channels, nuclear hormone receptors, catalytic receptors, enzymes and transporters. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading. The landscape format of the Concise Guide is designed to facilitate comparison of related targets from material contemporary to mid-2021, and supersedes data presented in the 2019/20, 2017/18, 2015/16 and 2013/14 Concise Guides and previous Guides to Receptors and Channels. It is produced in close conjunction with the Nomenclature and Standards Committee of the International Union of Basic and Clinical Pharmacology (NC-IUPHAR), therefore, providing official IUPHAR classification and nomenclature for human drug targets, where appropriate.
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| 4. |
- Ray, Nicholas E. E., et al.
(författare)
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Spatial and temporal variability in summertime dissolved carbon dioxide and methane in temperate ponds and shallow lakes
- 2023
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Ingår i: Limnology and Oceanography. - : American Society of Limnology and Oceanography. - 0024-3590 .- 1939-5590. ; 68:7, s. 1530-1545
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Tidskriftsartikel (refereegranskat)abstract
- Small waterbodies have potentially high greenhouse gas emissions relative to their small footprint on the landscape, although there is high uncertainty in model estimates. Scaling their carbon dioxide (CO2) and methane (CH4) exchange with the atmosphere remains challenging due to an incomplete understanding and characterization of spatial and temporal variability in CO2 and CH4. Here, we measured partial pressures of CO2 (pCO2) and CH4 (pCH4) across 30 ponds and shallow lakes during summer in temperate regions of Europe and North America. We sampled each waterbody in three locations at three times during the growing season, and tested which physical, chemical, and biological characteristics related to the means and variability of pCO2 and pCH4 in space and time. Summer means of pCO2 and pCH4 were inversely related to waterbody size and positively related to floating vegetative cover; pCO2 was also positively related to dissolved phosphorus. Temporal variability in partial pressure in both gases weas greater than spatial variability. Although sampling on a single date was likely to misestimate mean seasonal pCO2 by up to 26%, mean seasonal pCH4 could be misestimated by up to 64.5%. Shallower systems displayed the most temporal variability in pCH4 and waterbodies with more vegetation cover had lower temporal variability. Inland waters remain one of the most uncertain components of the global carbon budget; understanding spatial and temporal variability will ultimately help us to constrain our estimates and inform research priorities.
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| 5. |
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The Seventeenth Data Release of the Sloan Digital Sky Surveys : Complete Release of MaNGA, MaStar, and APOGEE-2 Data
- 2022
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Ingår i: Astrophysical Journal Supplement Series. - : Institute of Physics (IOP). - 0067-0049 .- 1538-4365. ; 259:2
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Tidskriftsartikel (refereegranskat)abstract
- This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 survey that publicly releases infrared spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the subsurvey Time Domain Spectroscopic Survey data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey subsurvey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated value-added catalogs. This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper, Local Volume Mapper, and Black Hole Mapper surveys.
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| 6. |
- Bergemalm, Daniel, 1977-, et al.
(författare)
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Systemic Inflammation in Preclinical Ulcerative Colitis
- 2021
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Ingår i: Gastroenterology. - : AGA Institute. - 0016-5085 .- 1528-0012. ; 161:5, s. 1526-1539.e9
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Tidskriftsartikel (refereegranskat)abstract
- Background & Aims: Preclinical ulcerative colitis is poorly defined. We aimed to characterize the preclinical systemic inflammation in ulcerative colitis, using a comprehensive set of proteins.Methods: We obtained plasma samples biobanked from individuals who developed ulcerative colitis later in life (n = 72) and matched healthy controls (n = 140) within a population-based screening cohort. We measured 92 proteins related to inflammation using a proximity extension assay. The biologic relevance of these findings was validated in an inception cohort of patients with ulcerative colitis (n = 101) and healthy controls (n = 50). To examine the influence of genetic and environmental factors on these markers, a cohort of healthy twin siblings of patients with ulcerative colitis (n = 41) and matched healthy controls (n = 37) were explored.Results: Six proteins (MMP10, CXCL9, CCL11, SLAMF1, CXCL11 and MCP-1) were up-regulated (P < .05) in preclinical ulcerative colitis compared with controls based on both univariate and multivariable models. Ingenuity Pathway Analyses identified several potential key regulators, including interleukin-1β, tumor necrosis factor, interferon-gamma, oncostatin M, nuclear factor-κB, interleukin-6, and interleukin-4. For validation, we built a multivariable model to predict disease in the inception cohort. The model discriminated treatment-naïve patients with ulcerative colitis from controls with leave-one-out cross-validation (area under the curve = 0.92). Consistently, MMP10, CXCL9, CXCL11, and MCP-1, but not CCL11 and SLAMF1, were significantly up-regulated among the healthy twin siblings, even though their relative abundances seemed higher in incident ulcerative colitis.Conclusions: A set of inflammatory proteins are up-regulated several years before a diagnosis of ulcerative colitis. These proteins were highly predictive of an ulcerative colitis diagnosis, and some seemed to be up-regulated already at exposure to genetic and environmental risk factors.
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| 7. |
- Caizergues, Aude E., et al.
(författare)
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Does urbanisation lead to parallel demographic shifts across the world in a cosmopolitan plant?
- 2024
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 33:7
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Tidskriftsartikel (refereegranskat)abstract
- Urbanisation is occurring globally, leading to dramatic environmental changes that are altering the ecology and evolution of species. In particular, the expansion of human infrastructure and the loss and fragmentation of natural habitats in cities is predicted to increase genetic drift and reduce gene flow by reducing the size and connectivity of populations. Alternatively, the 'urban facilitation model' suggests that some species will have greater gene flow into and within cities leading to higher diversity and lower differentiation in urban populations. These alternative hypotheses have not been contrasted across multiple cities. Here, we used the genomic data from the GLobal Urban Evolution project (GLUE), to study the effects of urbanisation on non-adaptive evolutionary processes of white clover (Trifolium repens) at a global scale. We found that white clover populations presented high genetic diversity and no evidence of reduced Ne linked to urbanisation. On the contrary, we found that urban populations were less likely to experience a recent decrease in effective population size than rural ones. In addition, we found little genetic structure among populations both globally and between urban and rural populations, which showed extensive gene flow between habitats. Interestingly, white clover displayed overall higher gene flow within urban areas than within rural habitats. Our study provides the largest comprehensive test of the demographic effects of urbanisation. Our results contrast with the common perception that heavily altered and fragmented urban environments will reduce the effective population size and genetic diversity of populations and contribute to their isolation.
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| 8. |
- Ray, Nicholas E., et al.
(författare)
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A review of how we assess denitrification in oyster habitats and proposed guidelines for future studies
- 2021
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Ingår i: Limnology and Oceanography. - : Wiley. - 1541-5856. ; 19:10, s. 714-731
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Forskningsöversikt (refereegranskat)abstract
- Excess nitrogen (N) loading and resulting eutrophication plague coastal ecosystems globally. Much work is being done to remove N before it enters coastal receiving waters, yet these efforts are not enough. Novel techniques to remove N from within the coastal ecosystem are now being explored. One of these techniques involves using oysters and their habitats to remove N via denitrification. There is substantial interest in incorporating oyster-mediated enhancement of benthic denitrification into N management plans and trading schemes. Measuring denitrification, however, is expensive and time consuming. For large-scale adoption of oyster-mediated denitrification into nutrient management plans, we need an accurate model that can be applied across ecosystems. Despite significant effort to measure and report rates of denitrification in oyster habitats, we are unable to create such a model, due to methodological differences between studies, incomplete data reporting, and inconsistent measurements of environmental variables that may be used to predict denitrification. To make a model that can predict denitrification in oyster habitats a reality, a common sampling and reporting scheme is needed across studies. Here, we provide relevant background on how oysters may stimulate denitrification, and the importance of oyster-mediated denitrification in remediating excess N loading to coastal systems. We then summarize methods commonly used to measure denitrification in oyster habitats, discuss the importance of various environmental variables that may be useful for predicting denitrification, and present a set of guidelines for measuring denitrification in oyster habitats, allowing development of models to support incorporation of oyster-mediated denitrification into future policy decisions.
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| 9. |
- Ray, Nicholas E., et al.
(författare)
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Negligible Greenhouse Gas Release from Sediments in Oyster Habitats
- 2021
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 55:20, s. 14225-14233
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Tidskriftsartikel (refereegranskat)abstract
- After centuries of decline, oyster populations are now on the rise in coastal systems globally following aquaculture development and restoration efforts. Oysters regulate the biogeochemistry of coastal systems in part by promoting sediment nutrient recycling and removing excess nitrogen via denitrification. Less clear is how oysters alter sediment greenhouse gas (GHG) fluxes—an important consideration as oyster populations grow. Here, we show that sediments in oyster habitats produce carbon dioxide (CO2), with highest rates in spring (2396.91 ± 381.98 μmol CO2 m–2 h–1) following deposition of seasonal diatom blooms and in summer (2795.20 ± 307.55 μmol CO2 m–2 h–1) when temperatures are high. Sediments in oyster habitats also consistently released methane to the water column (725.94 ± 150.34 nmol CH4 m–2 h–1) with no seasonal pattern. Generally, oyster habitat sediments were a sink for nitrous oxide (N2O; −36.11 ± 7.24 nmol N2O m–2 h–1), only occasionally releasing N2O in spring. N2O release corresponded to high organic matter and dissolved nitrogen availability, suggesting denitrification as the production pathway. Despite potential CO2 production increases under aquaculture in some locations, we conclude that in temperate regions oysters have an overall negligible impact on sediment GHG cycling.
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| 10. |
- Ray, Nicholas E., et al.
(författare)
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The Role of Coastal Yedoma Deposits and Continental Shelf Sediments in the Arctic Ocean Silicon Cycle
- 2024
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Ingår i: Global Biogeochemical Cycles. - 0886-6236 .- 1944-9224. ; 38:1
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Tidskriftsartikel (refereegranskat)abstract
- The availability of silicon (Si) in the ocean plays an important role in regulating biogeochemical and ecological processes. The Si budget of the Arctic Ocean appears balanced, with inputs equivalent to outputs, though it is unclear how a changing climate might aggravate this balance. In this study, we focus on Si cycling in Arctic coastal areas and continental shelf sediments to better constrain the Arctic Ocean Si budget. We provide the first estimate of amorphous Si (ASi) loading from erosion of coastal Yedoma deposits (30-90 Gmol yr-1), demonstrating comparable rates to particulate Si loading from rivers (10-90 Gmol yr-1). We found a positive relationship between surface sediment ASi and organic matter content on continental shelves. Combining these values with published Arctic shelf sediment properties and burial rates we estimate 70 Gmol Si yr-1 is buried on Arctic continental shelves, equivalent to 4.5% of all Si inputs to the Arctic Ocean. Sediment dissolved Si fluxes increased with distance from river mouths along cruise transects of shelf regions influenced by major rivers in the Laptev and East Siberian seas. On an annual basis, we estimate that Arctic shelf sediments recycle approximately up to twice as much DSi (680 Gmol Si) as is loaded from rivers (340-500 Gmol Si). Coastal erosion loads 30-90 Gmol Si yr-1 to the Arctic Ocean in the form of amorphous siliconContinental shelf sediments in the Arctic Ocean recycle more silicon than is loaded from riversApproximately 4.5% of silicon loaded on the Arctic Ocean is buried in continental shelf sediments
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| 11. |
- Wild, Birgit, et al.
(författare)
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Nitrous Oxide Dynamics in the Siberian Arctic Ocean and Vulnerability to Climate Change
- 2023
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Ingår i: Journal of Geophysical Research - Biogeosciences. - 2169-8953 .- 2169-8961. ; 128:5
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Tidskriftsartikel (refereegranskat)abstract
- Nitrous oxide (N2O) is a strong greenhouse gas and stratospheric ozone-depleting substance. Around 20% of global emissions stem from the ocean, but current estimates and future projections are uncertain due to poor spatial coverage over large areas and limited understanding of drivers of N2O dynamics. Here, we focus on the extensive and particularly data-lean Arctic Ocean shelves north of Siberia that experience rapid warming and increasing input of land-derived nitrogen with permafrost thaw. We combine water column N2O measurements from two expeditions with on-board incubation of intact sediment cores to assess N2O dynamics and the impact of land-derived nitrogen. Elevated nitrogen concentrations in water column and sediments were observed near large river mouths. Concentrations of N2O were only weakly correlated with dissolved nitrogen and turbidity, reflecting particulate matter from rivers and coastal erosion, and correlations varied between river plumes. Surface water N2O concentrations were on average close to equilibrium with the atmosphere, but varied widely (N2O saturation 38%-180%), indicating strong local N2O sources and sinks. Water column N2O profiles and low sediment-water N2O fluxes do not support strong sedimentary sources or sinks. We suggest that N2O dynamics in the region are influenced by water column N2O consumption under aerobic conditions or in anoxic microsites of particles, and possibly also by water column N2O production. Changes in biogeochemical and physical conditions will likely alter N2O dynamics in the Siberian Arctic Ocean over the coming decades, in addition to reduced N2O solubility in a warmer ocean.
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| 12. |
- Wilson, Samuel T., et al.
(författare)
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Ideas and perspectives : A strategic assessment of methane and nitrous oxide measurements in the marine environment
- 2020
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Ingår i: Biogeosciences. - : Copernicus GmbH. - 1726-4170 .- 1726-4189. ; 17:22, s. 5809-5828
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Tidskriftsartikel (refereegranskat)abstract
- In the current era of rapid climate change, accurate characterization of climate-relevant gas dynamics – namely production, consumption, and net emissions – is required for all biomes, especially those ecosystems most susceptible to the impact of change. Marine environments include regions that act as net sources or sinks for numerous climate-active trace gases including methane (CH4) and nitrous oxide (N2O). The temporal and spatial distributions of CH4 and N2O are controlled by the interaction of complex biogeochemical and physical processes. To evaluate and quantify how these mechanisms affect marine CH4 and N2O cycling requires a combination of traditional scientific disciplines including oceanography, microbiology, and numerical modeling. Fundamental to these efforts is ensuring that the datasets produced by independent scientists are comparable and interoperable. Equally critical is transparent communication within the research community about the technical improvements required to increase our collective understanding of marine CH4 and N2O. A workshop sponsored by Ocean Carbon and Biogeochemistry (OCB) was organized to enhance dialogue and collaborations pertaining to marine CH4 and N2O. Here, we summarize the outcomes from the workshop to describe the challenges and opportunities for near-future CH4 and N2O research in the marine environment.
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