| 1. |
- Rajewsky, N., et al.
(författare)
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LifeTime and improving European healthcare through cell-based interceptive medicine
- 2020
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Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 587:7834, s. 377-386
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Tidskriftsartikel (refereegranskat)abstract
- LifeTime aims to track, understand and target human cells during the onset and progression of complex diseases and their response to therapy at single-cell resolution. This mission will be implemented through the development and integration of single-cell multi-omics and imaging, artificial intelligence and patient-derived experimental disease models during progression from health to disease. Analysis of such large molecular and clinical datasets will discover molecular mechanisms, create predictive computational models of disease progression, and reveal new drug targets and therapies. Timely detection and interception of disease embedded in an ethical and patient-centered vision will be achieved through interactions across academia, hospitals, patient-associations, health data management systems and industry. Applying this strategy to key medical challenges in cancer, neurological, infectious, chronic inflammatory and cardiovascular diseases at the single-cell level will usher in cell-based interceptive medicine in Europe over the next decade.
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| 2. |
- Datry, T., et al.
(författare)
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A global analysis of terrestrial plant litter dynamics in non-perennial waterways
- 2018
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Ingår i: Nature Geoscience. - : Nature Publishing Group. - 1752-0894 .- 1752-0908. ; 11:7, s. 497-503
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Tidskriftsartikel (refereegranskat)abstract
- Perennial rivers and streams make a disproportionate contribution to global carbon (C) cycling. However, the contribution of intermittent rivers and ephemeral streams (IRES), which sometimes cease to flow and can dry completely, is largely ignored although they represent over half the global river network. Substantial amounts of terrestrial plant litter (TPL) accumulate in dry riverbeds and, upon rewetting, this material can undergo rapid microbial processing. We present the results of a global research collaboration that collected and analysed TPL from 212 dry riverbeds across major environmental gradients and climate zones. We assessed litter decomposability by quantifying the litter carbon-to-nitrogen ratio and oxygen (O2) consumption in standardized assays and estimated the potential short-term CO2 emissions during rewetting events. Aridity, cover of riparian vegetation, channel width and dry-phase duration explained most variability in the quantity and decomposability of plant litter in IRES. Our estimates indicate that a single pulse of CO2 emission upon litter rewetting contributes up to 10% of the daily CO2 emission from perennial rivers and stream, particularly in temperate climates. This indicates that the contributions of IRES should be included in global C-cycling assessments.
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| 3. |
- Akiba, K., et al.
(författare)
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The LHCb VELO Upgrade module construction
- 2024
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Ingår i: Journal of Instrumentation. - : Institute of Physics Publishing (IOPP). - 1748-0221. ; 19:6
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Tidskriftsartikel (refereegranskat)abstract
- The LHCb detector has undergone a major upgrade for LHC Run 3. This Upgrade I detector facilitates operation at higher luminosity and utilises full-detector information at the LHC collision rate, critically including the use of vertex information. A new vertex locator system, the VELO Upgrade, has been constructed. The core element of the new VELO are the double-sided pixelated hybrid silicon detector modules which operate in vacuum close to the LHC beam in a high radiation environment. The construction and quality assurance tests of these modules are described in this paper. The modules incorporate 200 mu m thick, n -on -p silicon sensors bump-bonded to 130 nm technology ASICs. These are attached with high precision to a silicon microchannel substrate that uses evaporative CO 2 cooling. The ASICs are controlled and read out with flexible printed circuits that are glued to the substrate and wire -bonded to the chips. The mechanical support of the module is given by a carbon fibre plate, two carbon fibre rods and an aluminium plate. The sensor attachment was achieved with an average precision of 21 mu m, more than 99.5% of all pixels are fully functional, and a thermal figure of merit of 3 Kcm 2 W - 1 was achieved. The production of the modules was successfully completed in 2021, with the final assembly and installation completed in time for data taking in 2022.
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| 4. |
- von Schiller, D., et al.
(författare)
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Sediment Respiration Pulses in Intermittent Rivers and Ephemeral Streams
- 2019
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Ingår i: Global Biogeochemical Cycles. - : American Geophysical Union (AGU). - 0886-6236 .- 1944-9224. ; 33:10, s. 1251-1263
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Tidskriftsartikel (refereegranskat)abstract
- Intermittent rivers and ephemeral streams (IRES) may represent over half the global stream network, but their contribution to respiration and carbon dioxide (CO2) emissions is largely undetermined. In particular, little is known about the variability and drivers of respiration in IRES sediments upon rewetting, which could result in large pulses of CO2. We present a global study examining sediments from 200 dry IRES reaches spanning multiple biomes. Results from standardized assays show that mean respiration increased 32-fold to 66-fold upon sediment rewetting. Structural equation modeling indicates that this response was driven by sediment texture and organic matter quantity and quality, which, in turn, were influenced by climate, land use, and riparian plant cover. Our estimates suggest that respiration pulses resulting from rewetting of IRES sediments could contribute significantly to annual CO2 emissions from the global stream network, with a single respiration pulse potentially increasing emission by 0.2-0.7%. As the spatial and temporal extent of IRES increases globally, our results highlight the importance of recognizing the influence of wetting-drying cycles on respiration and CO2 emissions in stream networks.
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| 5. |
- Sungnak, W., et al.
(författare)
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SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes
- 2020
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Ingår i: Nature Medicine. - : Nature Research. - 1078-8956 .- 1546-170X. ; 26:5, s. 681-687
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Tidskriftsartikel (refereegranskat)abstract
- We investigated SARS-CoV-2 potential tropism by surveying expression of viral entry-associated genes in single-cell RNA-sequencing data from multiple tissues from healthy human donors. We co-detected these transcripts in specific respiratory, corneal and intestinal epithelial cells, potentially explaining the high efficiency of SARS-CoV-2 transmission. These genes are co-expressed in nasal epithelial cells with genes involved in innate immunity, highlighting the cells’ potential role in initial viral infection, spread and clearance. The study offers a useful resource for further lines of inquiry with valuable clinical samples from COVID-19 patients and we provide our data in a comprehensive, open and user-friendly fashion at www.covid19cellatlas.org.
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| 6. |
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| 7. |
- Uy, G. L., et al.
(författare)
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Contribution of chemotherapy mobilization to disease control in multiple myeloma treated with autologous hematopoietic cell transplantation
- 2015
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Ingår i: Bone Marrow Transplantation. - : Springer Science and Business Media LLC. - 0268-3369 .- 1476-5365. ; 50:12, s. 1513-1518
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Tidskriftsartikel (refereegranskat)abstract
- In patients with multiple myeloma (MM) undergoing autologous hematopoietic cell transplantation (auto-HCT), peripheral blood progenitor cells may be collected following mobilization with growth factor alone (GF) or cytotoxic chemotherapy plus GF (CC+GF). It is uncertain whether the method of mobilization affects post-transplant outcomes. We compared these mobilization strategies in a retrospective analysis of 968 patients with MM from the Center for International Blood and Marrow Transplant Research database who received an auto-Ha in the US and Canada between 2007 and 2012. The kinetics of neutrophil engraftment (>= 0.5 x 10(9)/L) was similar between groups (13 vs 13 days, P=0.69) while platelet engraftment (>= 20 x 10(9)/L) was slightly faster with CC+GF (19 vs 18 days, P=0.006). Adjusted 3-year PFS was 43% (95% confidence interval (CI) 38-48) in GF and 40% (95% CI 35-45) in CC+GF, P=0.33. Adjusted 3-year OS was 82% (95% CI 78-86) vs 80% (95% CI 75-84), P=0.43 and adjusted 5-year OS was 62% (95% CI 54-68) vs 60% (95% CI 52-67), P=0.76, for GF and CC+GF, respectively. We conclude that MM patients undergoing auto-Ha have similar outcomes irrespective of the method of mobilization and found no evidence that the addition of chemotherapy to mobilization contributes to disease control.
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| 8. |
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| 9. |
- Sikkema, Lisa, et al.
(författare)
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An integrated cell atlas of the lung in health and disease
- 2023
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Ingår i: Nature Medicine. - : Springer Nature. - 1078-8956 .- 1546-170X. ; 29:6, s. 1563-1577
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Tidskriftsartikel (refereegranskat)abstract
- Single-cell technologies have transformed our understanding of human tissues. Yet, studies typically capture only a limited number of donors and disagree on cell type definitions. Integrating many single-cell datasets can address these limitations of individual studies and capture the variability present in the population. Here we present the integrated Human Lung Cell Atlas (HLCA), combining 49 datasets of the human respiratory system into a single atlas spanning over 2.4 million cells from 486 individuals. The HLCA presents a consensus cell type re-annotation with matching marker genes, including annotations of rare and previously undescribed cell types. Leveraging the number and diversity of individuals in the HLCA, we identify gene modules that are associated with demographic covariates such as age, sex and body mass index, as well as gene modules changing expression along the proximal-to-distal axis of the bronchial tree. Mapping new data to the HLCA enables rapid data annotation and interpretation. Using the HLCA as a reference for the study of disease, we identify shared cell states across multiple lung diseases, including SPP1 + profibrotic monocyte-derived macrophages in COVID-19, pulmonary fibrosis and lung carcinoma. Overall, the HLCA serves as an example for the development and use of large-scale, cross-dataset organ atlases within the Human Cell Atlas.
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| 10. |
- Aaij, R., et al.
(författare)
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Measurement of antiproton production from antihyperon decays in pHe collisions at √ˆšsNN=110 GeV
- 2023
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Ingår i: European Physical Journal C. - : SPRINGER. - 1434-6044 .- 1434-6052. ; 83
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Tidskriftsartikel (refereegranskat)abstract
- The interpretation of cosmic antiproton flux measurements from space-borne experiments is currently limited by the knowledge of the antiproton production cross-section in collisions between primary cosmic rays and the interstellar medium. Using collisions of protons with an energy of 6.5 TeV incident on helium nuclei at rest in the proximity of the interaction region of the LHCb experiment, the ratio of antiprotons originating from antihyperon decays to prompt production is measured for antiproton momenta between 12 and 110 GeV/c. The dominant antihyperon contribution, namely (Lambda) over bar -> (p) over bar pi(+) decays from promptly produced (Lambda) over bar particles, is also exclusively measured. The results complement the measurement of prompt antiproton production obtained from the same data sample. At the energy scale of this measurement, the antihyperon contributions to antiproton production are observed to be significantly larger than predictions of commonly used hadronic production models.
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| 11. |
- Aaij, R., et al.
(författare)
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Measurement of the Λb0 → Λ(1520)Ό+Ό- Differential Branching Fraction
- 2023
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Ingår i: Physical Review Letters. - : American Physical Society. - 0031-9007 .- 1079-7114. ; 131:15
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Tidskriftsartikel (refereegranskat)abstract
- The branching fraction of the rare decay Lambda(0 )(b)-> Lambda(1520)mu(+)mu(-) is measured for the first time, in the squared dimuon mass intervals q(2), excluding the J/psi and psi(2S) regions. The data sample analyzed was collected by the LHCb experiment at center-of-mass energies of 7, 8, and 13 TeV, corresponding to a total integrated luminosity of 9 fb(-1). The result in the highest q(2) interval, q(2) > 15.0 GeV2/c(4), where theoretical predictions have the smallest model dependence, agrees with the predictions.
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| 12. |
- Aaij, R., et al.
(författare)
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Model-independent measurement of charm mixing parameters in B → D0(→ K0Sπ+π- )Ό-ΜΌX decays
- 2023
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Ingår i: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 108:5
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Tidskriftsartikel (refereegranskat)abstract
- A measurement of charm mixing and CP-violating parameters is reported, using B over bar -> D0(-> K0S pi+pi-)x mu- nu over bar mu X decays reconstructed in proton-proton collisions collected by the LHCb experiment during the years 2016 to 2018, corresponding to an integrated luminosity of 5.4 fb-1. The measured mixing and CP-violating parameters are xCP = [4.29 1 1.48(stat) 1 0.26(syst)] x 10-3, yCP = [12.61 1 3.12(stat) 1 0.83(syst)] x 10-3, Ax = [-0.77 1 0.93(stat) 1 0.28(syst)] x 10-3, Ay = [3.01 1 1.92(stat) 1 0.26(syst)] x 10-3. The results are complementary to and consistent with previous measurements. A combination with the recent LHCb analysis of D*+ -> D0(-> K0S pi+ pi-)pi+ decays is reported.
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| 13. |
- Aaij, R., et al.
(författare)
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Search for the rare decays W+ →Ds+ ϒ and Z →D0 ϒ at LHCb
- 2023
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Ingår i: Chinese Physics C. - : Institute of Physics (IOP). - 1674-1137 .- 2058-6132. ; 47:9
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Tidskriftsartikel (refereegranskat)abstract
- A search for the rare decays W+ -> D-s(+)gamma and Z -> D-0 gamma and is performed using proton-proton collision data collected by the LHCb experiment at a centre-of-mass energy of 13TeV, corresponding to an integrated luminosity of 2.0fb(-1). No significant signal is observed for either decay mode and upper limits on their branching fractions are set using W+ -> mu(+)nu and Z ->mu(+)mu(-)decays as normalization channels. The upper limits are and at 95% confidence level for W+ -> D-s(+)gamma and Z -> D-0 gamma the and decay modes, respectively. This is the first reported search for Z -> D-0 gamma the decay, while the upper limit on the Z -> D-0 gamma branching fraction improves upon the previous best limit.
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| 14. |
- Aaij, R., et al.
(författare)
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Study of Bc+ meson decays to charmonia plus multihadron final states
- 2023
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Ingår i: Journal of High Energy Physics (JHEP). - : Springer. - 1126-6708 .- 1029-8479. ; :7
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Tidskriftsartikel (refereegranskat)abstract
- Four decay modes of the B-c(+) meson into a J/psi meson and multiple charged kaons or pions are studied using proton-proton collision data, collected with the LHCb detector at centre-of-mass energies of 7, 8, and 13TeV and corresponding to an integrated luminosity of 9 fb(-1). The decay B-c(+) -> J/psi K+ K- pi(+)pi(+)pi(-) is observed for the first time, and evidence for the B-c(+) -> J/psi 4 pi(+)3 pi(-) decay is found. The decay B-c(+) -> J/psi 3 pi(+)2 pi(-) is observed and the previous observation of the B-c(+) -> psi(2S)pi(+)pi(+)pi(-) decay is confirmed using the psi(2S) -> J/psi pi(+)pi(-) decay mode. Ratios of the branching fractions of these four B-c(+) decay channels are measured.
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| 15. |
- Aaij, R., et al.
(författare)
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Study of charmonium decays to KS0Kπ in the B → (KS0Kπ)K channels
- 2023
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Ingår i: Physical Review D. - : American Physical Society. - 2470-0010 .- 2470-0029. ; 108:3
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Tidskriftsartikel (refereegranskat)abstract
- A study of the B+ -> (KSK+)-K-0 K-pi(+) and B+ -> (KSK+K+)-K-0 pi(-) decays is performed using proton-proton collisions at center-of-mass energies of 7, 8 and 13 TeV at the LHCb experiment. The (KSK)-K-0 pi invariant mass spectra from both decay modes reveal a rich content of charmonium resonances. New precise measurements of the eta(c) and eta(c)(2S) resonance parameters are performed and branching fraction measurements are obtained for B+ decays to eta(c), J/psi, eta(c)(2S) and chi(c1) resonances. In particular, the first observation and branching fraction measurement of B+ -> chi K-c0(0)pi(+) is reported as well as first measurements of the B+ -> (KK+K-)-K-0 pi(+) and B+ -> (KK+K+)-K-0 pi(-) branching fractions. Dalitz plot analyses of eta(c) -> (KSK)-K-0 pi and eta(c)(2S) -> (KSK)-K-0 pi decays are performed. A new measurement of the amplitude and phase of the K pi S-wave as functions of the K pi mass is performed, together with measurements of the K-0*(1430), K-0*(1950) and a(0)(1700) parameters. Finally, the branching fractions of chi(c1) decays to K* resonances are also measured.
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| 16. |
- Aaij, R., et al.
(författare)
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Study of the B- → Λc+(Λ)over-barc-K- decay
- 2023
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Ingår i: Physical Review D. - : American Physical Society. - 2470-0010 .- 2470-0029. ; 108:1
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Tidskriftsartikel (refereegranskat)abstract
- The decay B- -> Lambda(+)(c)(Lambda) over bar K--(c)- is studied in proton-proton collisions at a center-of-mass energy of root s = 13 TeV using data corresponding to an integrated luminosity of 5 fb(-1) collected by the LHCb experiment. In the Lambda K-+(c)- system, the Xi(c)(2930)(0) state observed at the BABAR and Belle experiments is resolved into two narrower states, Xi(c)(2923)(0) and Xi(c)(2939)(0), whose masses and widths are measured to be m(Xi(c)(2930)(0) = 2924.5 +/- 0.4 +/- 1.1 Mev, m Xi(c)(2930)(0)) = 2938.5 +/- 0.9 +/- 2.3 Mev, Gamma(Xi(c)(2930)(0)) = 4.8 +/- 0.9 +/- 1.5 MeV, Gamma(Xi(c)(2930)(0) - 11.0 +/- 1.9 +/- 7.5 MeV, where the first uncertainties are statistical and the second systematic. The results are consistent with a previous LHCb measurement using a prompt Lambda K-+(c)- sample. Evidence of a new Xi(c)(2930)(0) state is found with a local significance of 3.8 sigma, whose mass and width are measured to be 2881.8 +/- 3.1 +/- 8.5 MeV and 12.4 +/- 5.3 +/- 5.8 MeV, respectively. In addition, evidence of a new decay mode Xi(c)(2930)(0) -> Lambda K-+(c) is found with a significance of 3.7 sigma. The relative branching fraction of B- -> Lambda(+)(c)(Lambda) over bar K--(c)- with respect to the B- -> D+D-K- decay is measured to be 2.36 +/- 0.11 +/- 0.22 +/- 0.25, where the first uncertainty is statistical, the second systematic and the third originates from the branching fractions of charm hadron decays.
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| 17. |
- Akiba, K., et al.
(författare)
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Measurement of thermal properties of the LHCb VELO detector using track-based software alignment
- 2023
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Ingår i: Journal of Instrumentation. - : Institute of Physics (IOP). - 1748-0221. ; 18:10
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Tidskriftsartikel (refereegranskat)abstract
- The thermal properties of the LHCb Vertex Locator (VELO) are studied using the real-time detector alignment procedure. The variation of the position and orientation of the detector elements as a function of the operating temperature of the VELO is presented. This study uses a dataset collected by the LHCb experiment during a VELO temperature scan performed at the end of LHC Run 2 (October 2018). Significant shrinkage of the VELO modules is observed at the operating temperature of -30(degrees)C compared to the laboratory measurements on a single module taken at a range of temperatures from +45(degrees)C to -25(degrees)C. The thermal shrinkage expected from the extrapolation of laboratory measurements to lower temperatures, and the results of this alignment study are in good agreement.
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| 18. |
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| 19. |
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| 20. |
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| 21. |
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| 22. |
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| 23. |
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| 24. |
- Catalan, N., et al.
(författare)
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Biodegradation kinetics of dissolved organic matter chromatographic fractions in an intermittent river
- 2017
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Ingår i: Journal of Geophysical Research - Biogeosciences. - : AMER GEOPHYSICAL UNION. - 2169-8953 .- 2169-8961. ; 122:1, s. 131-144
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Tidskriftsartikel (refereegranskat)abstract
- Controls on the degradation of dissolved organic matter (DOM) are complex but key to understand the role of freshwaters in the carbon cycle. Both the origin and previous degradation history have been suggested to determine DOM reactivity, but it is still a major challenge to understand the links between DOM composition and biodegradation kinetics. An appropriate context to study these links are intermittent rivers, as summer drought naturally diversifies DOM sources and sinks. Here we investigated the biodegradation kinetics of DOM in the main aquatic environments present in a temporary river. During dark incubations we traced the dynamics of bulk DOM and its main chromatographic fractions defined using LC-OCD: high molecular weight substances (HMWS), low molecular weight substances (LMWS), and humic substances and building blocks. Bulk DOM decay patterns were successfully fitted to the reactivity continuum (RC) biodegradation model. The RC parameters depicted running waters as the sites presenting a more reactive DOM, and temporary pools, enriched in leaf litter, as the ones with slowest DOM decay. The decay patterns of each DOM fraction were consistent throughout sites. LMWS and HMWS decayed in all cases and could be modeled using the RC model. Notably, the dynamics of LMWS controlled the bulk DOM kinetics. We discuss the mechanistic basis for the chromatographic fractions' kinetics during biodegradation and the implications that preconditioning and summer drought can have for DOM biodegradation in intermittent rivers.
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| 25. |
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