| 1. |
- Kanai, M, et al.
(författare)
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- 2023
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swepub:Mat__t
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| 2. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 3. |
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| 5. |
- Fowler, D., et al.
(författare)
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Atmospheric composition change : Ecosystems-Atmosphere interactions
- 2009
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Ingår i: Atmospheric Environment. - : Elsevier BV. - 1352-2310 .- 1873-2844. ; 43:33, s. 5193-5267
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Forskningsöversikt (refereegranskat)abstract
- Ecosystems and the atmosphere: This review describes the state of understanding the processes involved in the exchange of trace gases and aerosols between the earth's surface and the atmosphere. The gases covered include NO, NO2, HONO, HNO3, NH3, SO2, DMS, Biogenic VOC, O-3, CH4, N2O and particles in the size range 1 nm-10 mu m including organic and inorganic chemical species. The main focus of the review is on the exchange between terrestrial ecosystems, both managed and natural and the atmosphere, although some new developments in ocean-atmosphere exchange are included. The material presented is biased towards the last decade, but includes earlier work, where more recent developments are limited or absent. New methodologies and instrumentation have enabled, if not driven technical advances in measurement. These developments have advanced the process understanding and upscaling of fluxes, especially for particles, VOC and NH3. Examples of these applications include mass spectrometric methods, such as Aerosol Mass Spectrometry (AMS) adapted for field measurement of atmosphere-surface fluxes using micrometeorological methods for chemically resolved aerosols. Also briefly described are some advances in theory and techniques in micrometeorology. For some of the compounds there have been paradigm shifts in approach and application of both techniques and assessment. These include flux measurements over marine surfaces and urban areas using micrometeorological methods and the up-scaling of flux measurements using aircraft and satellite remote sensing. The application of a flux-based approach in assessment of O-3 effects on vegetation at regional scales is an important policy linked development secured through improved quantification of fluxes. The coupling of monitoring, modelling and intensive flux measurement at a continental scale within the NitroEurope network represents a quantum development in the application of research teams to address the underpinning science of reactive nitrogen in the cycling between ecosystems and the atmosphere in Europe. Some important developments of the science have been applied to assist in addressing policy questions, which have been the main driver of the research agenda, while other developments in understanding have not been applied to their wider field especially in chemistry-transport models through deficiencies in obtaining appropriate data to enable application or inertia within the modelling community. The paper identifies applications, gaps and research questions that have remained intractable at least since 2000 within the specialized sections of the paper, and where possible these have been focussed on research questions for the coming decade.
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| 10. |
- Mikkelsen, T N, et al.
(författare)
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Experimental design of multifactor climate change experiments with elevated CO2, warming and drought: the CLIMAITE project
- 2008
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Ingår i: Functional Ecology. - : Wiley. - 1365-2435 .- 0269-8463. ; 22:1, s. 185-195
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Tidskriftsartikel (refereegranskat)abstract
- Recent findings indicate that the interactions among CO2, temperature and water can be substantial, and that the combined effects on the biological systems of several factors may not be predicted from experiments with one or a few factors. Therefore realistic multifactorial experiments involving a larger set of main factors are needed. We describe a new Danish climate change-related field scale experiment, CLIMAITE, in a heath/grassland ecosystem. CLIMAITE is a full factorial combination of elevated CO2, elevated temperature and prolonged summer drought. The manipulations are intended to mimic anticipated major environmental changes at the site by year 2075 as closely as possible. The impacts on ecosystem processes and functioning (at ecophysiological levels, through responses by individuals and communities to ecosystem-level responses) are investigated simultaneously. The increase of [CO2] closely corresponds with the scenarios for year 2075, while the warming treatment is at the lower end of the predictions and seems to be the most difficult treatment to increase without unwanted side effects on the other variables. The drought treatment follows predictions of increased frequency of drought periods in summer. The combination of the treatments does not create new unwanted side effects on the treatments relative to the treatments alone.
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| 11. |
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| 12. |
- Timotijevic, L., et al.
(författare)
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Designing a research infrastructure (RI) on food behaviour and health : Balancing user needs, business model, governance mechanisms and technology
- 2021
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Ingår i: Trends in Food Science & Technology. - : Elsevier Ltd. - 0924-2244 .- 1879-3053. ; 116, s. 405-414
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Tidskriftsartikel (refereegranskat)abstract
- Background: A better understanding of food-related behaviour and its determinants can be achieved through harmonisation and linking of the various data-sources and knowledge platforms. Scope: We describe the key decision-making in the development of a prototype of the Determinants and Intake Platform (DI Platform), a data platform that aims to harmonise and link data on consumer food behaviour. It will be part of the Food Nutrition Health Research Infrastructure (FNH-RI) that will facilitate health, social and food sciences. Approach: The decision-making was based on the evidence of user needs and data characteristics that guided the specification of the key building blocks of the DI Platform. Eight studies were carried out, including consumer online survey; interview studies of key DI Platform stakeholders; desk research and workshops. Key findings: Consumers were most willing to share data with universities, then industry and government. Trust, risk perception and altruism predicted willingness to share. For most other stakeholders non-proprietary data was most likely to be shared. Lack of data standards, and incentives for sharing were the main barriers for sharing data among the key stakeholders. The value of various data types would hugely increase if linked with other sources. Finding the right balance between optimizing data sharing and minimizing ethical and legal risks was considered a key challenge. Conclusions: The development of DI Platform is based on careful balancing of the user, technical, business, legal and ethical requirements, following the FAIR principles and the need for financial sustainability, technical flexibility, transparency and multi-layered organisational governance.
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| 13. |
- Hartoog, O. E., et al.
(författare)
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VLT/X-Shooter spectroscopy of the afterglow of the Swift GRB 130606A Chemical abundances and reionisation at z similar to 6
- 2015
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 580
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Tidskriftsartikel (refereegranskat)abstract
- Context: The reionisation of the Universe is a process that is thought to have ended around z similar to 6, as inferred from spectroscopy of distant bright background sources, such as quasars (QSO) and gamma-ray burst (GRB) afterglows. Furthermore, spectroscopy of a GRB afterglow provides insight in its host galaxy, which is often too dim and distant to study otherwise.Aims: For the Swift GRB 130606A at z = 5.913 we have obtained a high S/N spectrum covering the full optical and near-IR wavelength region at intermediate spectral resolution with VLT/X-Shooter. We aim to measure the degree of ionisation of the intergalactic medium (IGM) between z = 5.02-5.84 and to study the chemical abundance pattern and dust content of its host galaxy.Methods: We estimated the UV continuum of the GRB afterglow using a power-law extrapolation, then measured the flux decrement due to absorption at Ly alpha,beta, and gamma wavelength regions. Furthermore, we fitted the shape of the red damping wing of Lya. The hydrogen and metal absorption lines formed in the host galaxy were fitted with Voigt profiles to obtain column densities. We investigated whether ionisation corrections needed to be applied.Results: Our measurements of the Ly alpha-forest optical depth are consistent with previous measurements of QSOs, but have a much smaller uncertainty. The analysis of the red damping wing yields a neutral fraction x(HI) < 0.05 (3 sigma). We obtain column density measurements of H, Al, Si, and Fe; for C, O, S and Ni we obtain limits. The ionisation due to the GRB is estimated to be negligible (corrections < 0.03 dex), but larger corrections may apply due to the pre-existing radiation field (up to 0.4 dex based on sub-DLA studies). Assuming that [Si/Fe] = +0.79 +/- 0.13 is due to dust depletion, the dust-to-metal ratio is similar to the Galactic value.Conclusions: Our measurements confirm that the Universe is already predominantly ionised over the redshift range probed in this work, but was slightly more neutral at z > 5.6. GRBs are useful probes of the ionisation state of the IGM in the early Universe, but because of internal scatter we need a larger statistical sample to draw robust conclusions. The high [Si/Fe] in the host can be due to dust depletion, a-element enhancement, or a combination of both. The very high value of [Al/Fe] = 2.40 +/- 0.78 might be due to a proton capture process and is probably connected to the stellar population history. We estimate the host metallicity to be -1.7 < [M/H] < -0.9 (2%-13% of solar).
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| 14. |
- Dos Santos, E. C., et al.
(författare)
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Ciprofloxacin intercalated in fluorohectorite clay : Identical pure drug activity and toxicity with higher adsorption and controlled release rate
- 2017
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Ingår i: RSC Advances. - : Royal Society of Chemistry (RSC). - 2046-2069. ; 7:43, s. 26537-26545
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Tidskriftsartikel (refereegranskat)abstract
- Different natural clay minerals, including halloysite, montmorillonite and kaolinite, have been proven to be efficient drug carriers providing for high and long lasting drug concentrations owing to their adsorption capacity and ion exchange property. Synthetic clays, however, are advantageous over the natural clay minerals in terms of purity of composition and controllable cation exchange capacity, factors that contribute to improve reproducibility of the host system. Here we studied a synthetic smectite clay as a candidate for high adsorption and controlled release rate. Via X-ray powder diffraction we verified that, under acidic conditions, the antibiotic ciprofloxacin was successfully incorporated in the synthetic clay fluorohectorite, while via UV-VIS spectroscopy we showed that the degree of the drug incorporation is at least 25% higher than for other systems reported in the literature. Furthermore, temperature dependent release studies allowed us to show that the release process is thermally activated and diffusion-controlled. Finally, via bacterial and toxicological tests, we demonstrated that the effectiveness and toxicity of pure ciprofloxacin is unaffected in the clay-drug complex.
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| 15. |
- Hait, A. S., et al.
(författare)
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Defects in LC3B2 and ATG4A underlie HSV2 meningitis and reveal a critical role for autophagy in antiviral defense in humans
- 2020
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Ingår i: Science Immunology. - : American Association for the Advancement of Science (AAAS). - 2470-9468. ; 5:54
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Tidskriftsartikel (refereegranskat)abstract
- Recurrent herpesvirus infections can manifest in different forms of disease, including cold sores, genital herpes, and encephalitis. There is an incomplete understanding of the genetic and immunological factors conferring susceptibility to recurrent herpes simplex virus 2 (HSV2) infection in the central nervous system (CNS). Here, we describe two adult patients with recurrent HSV2 lymphocytic Mollaret's meningitis that each carry a rare monoallelic variant in the autophagy proteins ATG4A or LC3B2. HSV2-activated autophagy was abrogated in patient primary fibroblasts, which also exhibited significantly increased viral replication and enhanced cell death. HSV2 antigen was captured in autophagosomes of infected cells, and genetic inhibition of autophagy by disruption of autophagy genes, including ATG4A and LC3B2, led to enhanced viral replication and cell death in primary fibroblasts and a neuroblastoma cell line. Activation of autophagy by HSV2 was sensitive to ultraviolet (UV) irradiation of the virus and inhibited in the presence of acyclovir, but HSV2-induced autophagy was independent of the DNA-activated STING pathway. Reconstitution of wild-type ATG4A and LC3B2 expression using lentiviral gene delivery or electroporation of in vitro transcribed mRNA into patient cells restored virus-induced autophagy and the ability to control HSV2 replication. This study describes a previously unknown link between defective autophagy and an inborn error of immunity that can lead to increased susceptibility to HSV2 infection, suggesting an important role for autophagy in antiviral immunity in the CNS.
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| 16. |
- Bronden, A., et al.
(författare)
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Glucose-lowering effects and mechanisms of the bile acid-sequestering resin sevelamer
- 2018
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Ingår i: Diabetes Obesity & Metabolism. - : Wiley. - 1462-8902 .- 1463-1326. ; 20:7, s. 1623-1631
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Tidskriftsartikel (refereegranskat)abstract
- Aims Sevelamer, a non-absorbable amine-based resin used for treatment of hyperphosphataemia, has been demonstrated to have a marked bile acid-binding potential alongside beneficial effects on lipid and glucose metabolism. The aim of this study was to investigate the glucose-lowering effect and mechanism(s) of sevelamer in patients with type 2 diabetes. Materials and Methods In this double-blinded randomized controlled trial, we randomized 30 patients with type 2 diabetes to sevelamer (n = 20) or placebo (n = 10). Participants were subjected to standardized 4-hour liquid meal tests at baseline and after 7 days of treatment. The main outcome measure was plasma glucagon-like peptide-1 excursions as measured by area under the curve. In addition, blood was sampled for measurements of glucose, lipids, glucose-dependent insulinotropic polypeptide, C-peptide, glucagon, fibroblast growth factor-19, cholecystokinin and bile acids. Assessments of gastric emptying, resting energy expenditure and gut microbiota composition were performed. Results Sevelamer elicited a significant placebo-corrected reduction in plasma glucose with concomitant reduced fibroblast growth factor-19 concentrations, increased de novo synthesis of bile acids, a shift towards a more hydrophilic bile acid pool and increased lipogenesis. No glucagon-like peptide-1-mediated effects on insulin, glucagon or gastric emptying were evident, which points to a limited contribution of this incretin hormone to the glucose-lowering effect of sevelamer. Furthermore, no sevelamer-mediated effects on gut microbiota composition or resting energy expenditure were observed. Conclusions Sevelamer reduced plasma glucose concentrations in patients with type 2 diabetes by mechanisms that seemed to involve decreased intestinal and hepatic bile acid-mediated farnesoid X receptor activation.
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| 17. |
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| 18. |
- Dzhigaev, D., et al.
(författare)
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Bragg coherent x-ray diffractive imaging of a single indium phosphide nanowire
- 2016
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Ingår i: Journal of Optics. - : IOP Publishing. - 2040-8978 .- 2040-8986. ; 18:6
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Tidskriftsartikel (refereegranskat)abstract
- Three-dimensional (3D) Bragg coherent x-ray diffractive imaging (CXDI) with a nanofocused beam was applied to quantitatively map the internal strain field of a single indium phosphide nanowire. The quantitative values of the strain were obtained by pre-characterization of the beam profile with transmission ptychography on a test sample. Our measurements revealed the 3D strain distribution in a region of 150 nm below the catalyst Au particle. We observed a slight gradient of the strain in the range of 0.6% along the [111] growth direction of the nanowire. We also determined the spatial resolution in our measurements to be about 10 nm in the direction perpendicular to the facets of the nanowire. The CXDI measurements were compared with the finite element method simulations and show a good agreement with our experimental results. The proposed approach can become an effective tool for in operando studies of the nanowires.
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| 19. |
- Gustafson, Johan, et al.
(författare)
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One-dimensional PtO(2) at Pt steps : Formation and reaction with CO
- 2005
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 95:25, s. 1-4
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Tidskriftsartikel (refereegranskat)abstract
- Using core-level spectroscopy and density functional theory we show that a one-dimensional (1D) PtO(2) oxide structure forms at the steps of the Pt(332) surface after O(2) exposure. The 1D oxide is found to be stable in an oxygen pressure range, where bulk oxides are only metastable, and is therefore argued to be a precursor to the Pt oxidation. As an example of the consequences of such a precursor exclusively present at the steps, we investigate the reaction of CO with oxygen covered Pt(332). Albeit more strongly bound, the oxidic oxygen is found to react more easily with CO than oxygen chemisorbed on the Pt terraces.
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| 20. |
- Ivanell, Stefan, et al.
(författare)
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Comparison between experiments and Large-Eddy Simulations of tip spiral structure and geometry
- 2015
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Ingår i: WAKE CONFERENCE 2015. - : IOP Publishing.
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Konferensbidrag (refereegranskat)abstract
- Results from Large-Eddy Simulations using the actuator line technique have been validated against experimental results. The experimental rotor wake, which forms the basis for the comparison, was studied in a recirculating free-surface water channel, where a helical vortex was generated by a single-bladed rotor mounted on a shaft. An investigation of how the experimental blade geometry and aerofoil characteristics affect the results was performed. Based on this, an adjustment of the pitch setting was introduced, which is still well within the limits of the experimental uncertainty. Excellent agreement between the experimental and the numerical results was achieved concerning the circulation, wake expansion and pitch of the helical tip vortex. A disagreement was found regarding the root vortex position and the axial velocity along the centre line of the tip vortex. This work establishes a good base for further studies of more fundamental stability parameters of helical rotor wakes.
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| 21. |
- Lin, Yan-Shih, et al.
(författare)
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Optimal stomatal behaviour around the world
- 2015
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Ingår i: Nature Climate Change. - : Springer Science and Business Media LLC. - 1758-678X .- 1758-6798. ; 5, s. 459-464
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Tidskriftsartikel (refereegranskat)abstract
- Stomatal conductance (gs) is a key land-surface attribute as it links transpiration, the dominant component of global land evapotranspiration, and photosynthesis, the driving force of the global carbon cycle. Despite the pivotal role of gs in predictions of global water and carbon cycle changes, a globalscale database and an associated globally applicable model of gs that allow predictions of stomatal behaviour are lacking. Here,we present a database of globally distributed gs obtained in the field for a wide range of plant functional types (PFTs) and biomes. We find that stomatal behaviour differs among PFTs according to their marginal carbon cost of water use, as predicted by the theory underpinning the optimal stomatal model1 and the leaf and wood economics spectrum2,3.We also demonstrate a global relationship with climate. These findings provide a robust theoretical framework for understanding and predicting the behaviour of gs across biomes and across PFTs that can be applied to regional, continental and global-scale modelling of ecosystem productivity, energy balance and ecohydrological processes in a future changing climate.
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| 22. |
- Lin, Yan-Shih, et al.
(författare)
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Optimal stomatal behaviour around the world
- 2015
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Ingår i: Nature Climate Change. - 1758-6798 .- 1758-678X. ; 5:5, s. 459-464
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Tidskriftsartikel (refereegranskat)abstract
- Stomatal conductance (g(s)) is a key land-surface attribute as it links transpiration, the dominant component of global land evapotranspiration, and photosynthesis, the driving force of the global carbon cycle. Despite the pivotal role of g(s) in predictions of global water and carbon cycle changes, a global-scale database and an associated globally applicable model of g(s) that allow predictions of stomatal behaviour are lacking. Here, we present a database of globally distributed g(s) obtained in the field for a wide range of plant functional types (PFTs) and biomes. We find that stomatal behaviour differs among PFTs according to their marginal carbon cost of water use, as predicted by the theory underpinning the optimal stomatal model(1) and the leaf and wood economics spectrum(2,3). We also demonstrate a global relationship with climate. These findin g(s) provide a robust theoretical framework for understanding and predicting the behaviour of g(s) across biomes and across PFTs that can be applied to regional, continental and global-scale modelling of ecosystem productivity, energy balance and ecohydrological processes in a future changing climate.
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