| 1. |
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| 2. |
- Algaba, Juan-Carlos, et al.
(author)
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Broadband Multi-wavelength Properties of M87 during the 2017 Event Horizon Telescope Campaign
- 2021
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In: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8213 .- 2041-8205. ; 911:1
-
Research review (peer-reviewed)abstract
- In 2017, the Event Horizon Telescope (EHT) Collaboration succeeded in capturing the first direct image of the center of the M87 galaxy. The asymmetric ring morphology and size are consistent with theoretical expectations for a weakly accreting supermassive black hole of mass ∼6.5 × 109 M o˙. The EHTC also partnered with several international facilities in space and on the ground, to arrange an extensive, quasi-simultaneous multi-wavelength campaign. This Letter presents the results and analysis of this campaign, as well as the multi-wavelength data as a legacy data repository. We captured M87 in a historically low state, and the core flux dominates over HST-1 at high energies, making it possible to combine core flux constraints with the more spatially precise very long baseline interferometry data. We present the most complete simultaneous multi-wavelength spectrum of the active nucleus to date, and discuss the complexity and caveats of combining data from different spatial scales into one broadband spectrum. We apply two heuristic, isotropic leptonic single-zone models to provide insight into the basic source properties, but conclude that a structured jet is necessary to explain M87's spectrum. We can exclude that the simultaneous γ-ray emission is produced via inverse Compton emission in the same region producing the EHT mm-band emission, and further conclude that the γ-rays can only be produced in the inner jets (inward of HST-1) if there are strongly particle-dominated regions. Direct synchrotron emission from accelerated protons and secondaries cannot yet be excluded.
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| 3. |
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| 4. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 5. |
- Birney, Ewan, et al.
(author)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Journal article (peer-reviewed)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 6. |
- Schönning, Karin, et al.
(author)
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Polarisation of the omega meson in the pd -> He-3 omega reaction at 1360 and 1450 MeV
- 2008
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In: Physics Letters B. - elsevier : Elsevier BV. - 0370-2693 .- 1873-2445. ; 668:4, s. 258-262
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Journal article (peer-reviewed)abstract
- The tensor polarisation of omega mesons produced in the pd -> He-3 omega reaction has been studied at two energies near threshold. The 3 He nuclei were detected in coincidence with the pi(0)pi(+)pi(-) or pi(0)gamma decay products of the omega. in contrast to the case of phi-meson production, the omega mesons are found to be unpolarised. This brings into question the applicability of the Okubo-Zweig-lizuka rule when comparing the production of vector mesons in low energy hadronic reactions.
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| 7. |
- Berlowski, M., et al.
(author)
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Measurement of eta meson decays into lepton-antilepton pairs
- 2008
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In: Physical Review D. Particles and fields. - : American Physical Society. - 0556-2821 .- 1089-4918. ; 77:3, s. 032004-
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Journal article (peer-reviewed)abstract
- A search for rare lepton decays of the eta meson was performed using the WASA detector at CELSIUS. Two candidates for double Dalitz decay eta -> e(+)e(-)e(+)e(-) events are reported with a background of 1.3 +/- 0.2 events. This allows to set an upper limit to the branching ratio of 9.7x10(-5) (90% CL). The branching ratio for the decay eta -> e(+)e(-)gamma is determined to (7.8 +/- 0.5(stat)+/- 0.8(syst))x10(-3) in agreement with world average value. An upper limit (90% CL) for the branching ratio for the eta -> e(+)e(-) decay is 2.7x10(-5) and a limit for the sum of the eta ->mu(+)mu(-)mu(+)mu(-) and eta ->pi(+)pi(-)mu(+)mu(-) decays is 3.6x10(-4).
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| 8. |
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| 9. |
- Bargholtz, Chr., et al.
(author)
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Measurement of the eta -> pi(+)pi(-)e(+)e(-) decay branching ratio
- 2007
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In: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 644:5-6, s. 299-303
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Journal article (peer-reviewed)abstract
- The reaction pd -> He-3 eta at threshold was used to provide a clean source of eta mesons for decay studies with the WASA detector at CELSIUS. The branching ratio of the decay eta -> pi(+)pi(-)e(+)e(-) is measured to be (4.3 +/- 1.3 +/- 0.4) x 10(-4).
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| 10. |
- Bluhm, Marcus, et al.
(author)
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Dynamics of critical fluctuations : Theory - phenomenology - heavy-ion collisions
- 2020
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In: Nuclear Physics A. - : ELSEVIER. - 0375-9474 .- 1873-1554. ; 1003
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Journal article (peer-reviewed)abstract
- This report summarizes the presentations and discussions during the Rapid Reaction Task Force "Dynamics of critical fluctuations: Theory - phenomenology - heavy-ion collisions", which was organized by the ExtreMe Matter Institute EMMI and held at GSI, Darmstadt, Germany in April 2019. We address the current understanding of the dynamics of critical fluctuations in QCD and their measurement in heavy-ion collision experiments. In addition, we outline what might be learned from studying correlations in other physical systems, such as cold atomic gases.
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| 11. |
- Frieler, Katja, et al.
(author)
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Scenario setup and forcing data for impact model evaluation and impact attribution within the third round of the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP3a)
- 2024
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In: Geoscientific Model Development. - : Copernicus Publications. - 1991-959X .- 1991-9603. ; 17:1, s. 1-51
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Journal article (peer-reviewed)abstract
- This paper describes the rationale and the protocol of the first component of the third simulation round of the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP3a, http://www.isimip.org, last access: 2 November 2023) and the associated set of climate-related and direct human forcing data (CRF and DHF, respectively). The observation-based climate-related forcings for the first time include high-resolution observational climate forcings derived by orographic downscaling, monthly to hourly coastal water levels, and wind fields associated with historical tropical cyclones. The DHFs include land use patterns, population densities, information about water and agricultural management, and fishing intensities. The ISIMIP3a impact model simulations driven by these observation-based climate-related and direct human forcings are designed to test to what degree the impact models can explain observed changes in natural and human systems. In a second set of ISIMIP3a experiments the participating impact models are forced by the same DHFs but a counterfactual set of atmospheric forcings and coastal water levels where observed trends have been removed. These experiments are designed to allow for the attribution of observed changes in natural, human, and managed systems to climate change, rising CH4 and CO2 concentrations, and sea level rise according to the definition of the Working Group II contribution to the IPCC AR6.
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| 12. |
- Föhl, K, et al.
(author)
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The WASA focussing light guide disc DIRC
- 2012
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In: Journal of Instrumentation. - 1748-0221. ; 7, s. C01002-
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Journal article (peer-reviewed)abstract
- Two Disc DIRC prototypes have been designed and built and are shortly being tested with proton test beams. Different in design details, both aim to provide the WASA-at-COSY experiment with a particle velocity measurement that improves the missing mass resolution. This paper shows the difference in concept between these two designs and also compares to designs that have been proposed for PANDA.
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| 13. |
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| 14. |
- Rada-Iglesias, Alvaro, et al.
(author)
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Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes
- 2007
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In: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 17:6, s. 708-719
-
Journal article (peer-reviewed)abstract
- Butyrate is a histone deacetylase inhibitor (HDACi) with anti-neoplastic properties, which theoretically reactivates epigenetically silenced genes by increasing global histone acetylation. However, recent studies indicate that a similar number or even more genes are down-regulated than up-regulated by this drug. We treated hepatocarcinoma HepG2 cells with butyrate and characterized the levels of acetylation at DNA-bound histones H3 and H4 by ChIP-chip along the ENCODE regions. In contrast to the global increases of histone acetylation, many genomic regions close to transcription start sites were deacetylated after butyrate exposure. In order to validate these findings, we found that both butyrate and trichostatin A treatment resulted in histone deacetylation at selected regions, while nucleosome loss or changes in histone H3 lysine 4 trimethylation (H3K4me3) did not occur in such locations. Furthermore, similar histone deacetylation events were observed when colon adenocarcinoma HT-29 cells were treated with butyrate. In addition, genes with deacetylated promoters were down-regulated by butyrate, and this was mediated at the transcriptional level by affecting RNA polymerase II (POLR2A) initiation/elongation. Finally, the global increase in acetylated histones was preferentially localized to the nuclear periphery, indicating that it might not be associated to euchromatin. Our results are significant for the evaluation of HDACi as anti-tumourogenic drugs, suggesting that previous models of action might need to be revised, and provides an explanation for the frequently observed repression of many genes during HDACi treatment.
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| 15. |
- Al-Chalabi, Ammar, et al.
(author)
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July 2017 ENCALS statement on edaravone
- 2017
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In: Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration. - : TAYLOR & FRANCIS LTD. - 2167-8421 .- 2167-9223. ; 18:7-8, s. 471-474
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Journal article (peer-reviewed)abstract
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| 16. |
- Franke, James A., et al.
(author)
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The GGCMI Phase 2 experiment : Global gridded crop model simulations under uniform changes in CO2, temperature, water, and nitrogen levels (protocol version 1.0)
- 2020
-
In: Geoscientific Model Development. - : Copernicus GmbH. - 1991-959X .- 1991-9603. ; 13:5, s. 2315-2336
-
Journal article (peer-reviewed)abstract
- Concerns about food security under climate change motivate efforts to better understand future changes in crop yields. Process-based crop models, which represent plant physiological and soil processes, are necessary tools for this purpose since they allow representing future climate and management conditions not sampled in the historical record and new locations to which cultivation may shift. However, process-based crop models differ in many critical details, and their responses to different interacting factors remain only poorly understood. The Global Gridded Crop Model Intercomparison (GGCMI) Phase 2 experiment, an activity of the Agricultural Model Intercomparison and Improvement Project (AgMIP), is designed to provide a systematic parameter sweep focused on climate change factors and their interaction with overall soil fertility, to allow both evaluating model behavior and emulating model responses in impact assessment tools. In this paper we describe the GGCMI Phase 2 experimental protocol and its simulation data archive. A total of 12 crop models simulate five crops with systematic uniform perturbations of historical climate, varying CO2, temperature, water supply, and applied nitrogen ("CTWN") for rainfed and irrigated agriculture, and a second set of simulations represents a type of adaptation by allowing the adjustment of growing season length. We present some crop yield results to illustrate general characteristics of the simulations and potential uses of the GGCMI Phase 2 archive. For example, in cases without adaptation, modeled yields show robust decreases to warmer temperatures in almost all regions, with a nonlinear dependence that means yields in warmer baseline locations have greater temperature sensitivity. Inter-model uncertainty is qualitatively similar across all the four input dimensions but is largest in high-latitude regions where crops may be grown in the future.
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| 17. |
- Ghiringhelli, Luca M., et al.
(author)
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Shared metadata for data-centric materials science
- 2023
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In: Scientific Data. - : NATURE PORTFOLIO. - 2052-4463. ; 10
-
Journal article (other academic/artistic)abstract
- The expansive production of data in materials science, their widespread sharing and repurposing requires educated support and stewardship. In order to ensure that this need helps rather than hinders scientific work, the implementation of the FAIR-data principles (Findable, Accessible, Interoperable, and Reusable) must not be too narrow. Besides, the wider materials-science community ought to agree on the strategies to tackle the challenges that are specific to its data, both from computations and experiments. In this paper, we present the result of the discussions held at the workshop on “Shared Metadata and Data Formats for Big-Data Driven Materials Science”. We start from an operative definition of metadata, and the features that a FAIR-compliant metadata schema should have. We will mainly focus on computational materials-science data and propose a constructive approach for the FAIRification of the (meta)data related to ground-state and excited-states calculations, potential-energy sampling, and generalized workflows. Finally, challenges with the FAIRification of experimental (meta)data and materials-science ontologies are presented together with an outlook of how to meet them.
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| 18. |
- Monteil, Guillaume, et al.
(author)
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The regional European atmospheric transport inversion comparison, EUROCOM : First results on European-wide terrestrial carbon fluxes for the period 2006-2015
- 2020
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In: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 20:20, s. 12063-12091
-
Journal article (peer-reviewed)abstract
- Atmospheric inversions have been used for the past two decades to derive large-scale constraints on the sources and sinks of CO2 into the atmosphere. The development of dense in situ surface observation networks, such as ICOS in Europe, enables in theory inversions at a resolution close to the country scale in Europe. This has led to the development of many regional inversion systems capable of assimilating these high-resolution data, in Europe and elsewhere. The EUROCOM (European atmospheric transport inversion comparison) project is a collaboration between seven European research institutes, which aims at producing a collective assessment of the net carbon flux between the terrestrial ecosystems and the atmosphere in Europe for the period 2006 2015. It aims in particular at investigating the capacity of the inversions to deliver consistent flux estimates from the country scale up to the continental scale. The project participants were provided with a common database of in situ-observed CO2 concentrations (including the observation sites that are now part of the ICOS network) and were tasked with providing their best estimate of the net terrestrial carbon flux for that period, and for a large domain covering the entire European Union. The inversion systems differ by the transport model, the inversion approach, and the choice of observation and prior constraints, enabling us to widely explore the space of uncertainties. This paper describes the intercomparison protocol and the participating systems, and it presents the first results from a reference set of inversions, at the continental scale and in four large regions. At the continental scale, the regional inversions support the assumption that European ecosystems are a relatively small sink (-0:21 ± 0:2 Pg C yr-1). We find that the convergence of the regional inversions at this scale is not better than that obtained in state-of-the-art global inversions. However, more robust results are obtained for subregions within Europe, and in these areas with dense observational coverage, the objective of delivering robust countryscale flux estimates appears achievable in the near future.
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| 19. |
- Petrén, Henrik, et al.
(author)
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eta-meson production in proton-proton collisions at excess energies of 40 and 72 MeV
- 2010
-
In: Physical Review C. Nuclear Physics. - 0556-2813 .- 1089-490X. ; 82:5, s. 055206-
-
Journal article (peer-reviewed)abstract
- The production of eta mesons in proton-proton collisions has been studied using the WASA detector at the CELSIUS storage ring at excess energies of Q = 40 MeV and Q = 72 MeV. The eta was detected through its 2 gamma decay in a near-4 pi electromagnetic calorimeter, whereas the protons were measured by a combination of straw chambers and plastic scintillator planes in the forward hemisphere. About 6.9 x 10(4) and 9.3 x 10(4) events were found at Q = 40 MeV and Q = 72 MeV, respectively, with background contributions of less than 5%. A simple parametrization of the production cross section in terms of low partial waves was used to evaluate the acceptance corrections. Strong evidence was found for the influence of higher partial waves. The Dalitz plots show the presence of p waves in both the pp and the eta {pp} systems and the angular distributions of the eta in the center-of-mass frame suggest the influence of d-wave eta mesons.
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| 20. |
- Pieber, Simone M., et al.
(author)
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Analysis of regional CO2contributions at the high Alpine observatory Jungfraujoch by means of atmospheric transport simulations and δ13C
- 2022
-
In: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 22:16, s. 10721-10749
-
Journal article (peer-reviewed)abstract
- In this study, we investigated the regional contributions of carbon dioxide (CO2) at the location of the high Alpine observatory Jungfraujoch (JFJ, Switzerland, 3580ĝ€¯mĝ€¯a.s.l.). To this purpose, we combined receptor-oriented atmospheric transport simulations for CO2 concentration in the period 2009-2017 with stable carbon isotope (δ13C-CO2) information. We applied two Lagrangian particle dispersion models driven by output from two different numerical weather prediction systems (FLEXPART-COSMO and STILT-ECMWF) in order to simulate CO2 concentration at JFJ based on regional CO2 fluxes, to estimate atmospheric δ13C-CO2, and to obtain model-based estimates of the mixed source signatures (δ13Cm). Anthropogenic fluxes were taken from a fuel-type-specific version of the EDGAR v4.3 inventory, while ecosystem fluxes were based on the Vegetation Photosynthesis and Respiration Model (VPRM). The simulations of CO2, δ13C-CO2, and δ13Cm were then compared to observations performed by quantum cascade laser absorption spectroscopy. The models captured around 40ĝ€¯% of the regional CO2 variability above or below the large-scale background and up to 35ĝ€¯% of the regional variability in δ13C-CO2. This is according to expectations considering the complex Alpine topography, the low intensity of regional signals at JFJ, and the challenging measurements. Best agreement between simulations and observations in terms of short-term variability and intensity of the signals for CO2 and δ13C-CO2 was found between late autumn and early spring. The agreement was inferior in the early autumn periods and during summer. This may be associated with the atmospheric transport representation in the models. In addition, the net ecosystem exchange fluxes are a possible source of error, either through inaccuracies in their representation in VPRM for the (Alpine) vegetation or through a day (uptake) vs. night (respiration) transport discrimination to JFJ. Furthermore, the simulations suggest that JFJ is subject to relatively small regional anthropogenic contributions due to its remote location (elevated and far from major anthropogenic sources) and the limited planetary boundary layer influence during winter. Instead, the station is primarily exposed to summertime ecosystem CO2 contributions, which are dominated by rather nearby sources (within 100ĝ€¯km). Even during winter, simulated gross ecosystem respiration accounted for approximately 50ĝ€¯% of all contributions to the CO2 concentrations above the large-scale background. The model-based monthly mean δ13Cm ranged from -ĝ€¯22ĝ€¯‰ in winter to -ĝ€¯28ĝ€¯‰ in summer and reached the most depleted values of -ĝ€¯35ĝ€¯‰ at higher fractions of natural gas combustion, as well as the most enriched values of -ĝ€¯17ĝ€¯‰ to -ĝ€¯12ĝ€¯‰ when impacted by cement production emissions. Observation-based δ13Cm values were derived independently from the simulations by a moving Keeling-plot approach. While model-based estimates spread in a narrow range, observation-based δ13Cm values exhibited a larger scatter and were limited to a smaller number of data points due to the stringent analysis prerequisites.
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| 21. |
- Rada-Iglesias, Alvaro, et al.
(author)
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Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays
- 2005
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In: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 14:22, s. 3435-3447
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Journal article (peer-reviewed)abstract
- We present a detailed in vivo characterization of hepatocyte transcriptional regulation in HepG2 cells, using chromatin immunoprecipitation and detection on PCR fragment-based genomic tiling path arrays covering the encyclopedia of DNA element (ENCODE) regions. Our data suggest that HNF-4α and HNF-3β, which were commonly bound to distal regulatory elements, may cooperate in the regulation of a large fraction of the liver transcriptome and that both HNF-4α and USF1 may promote H3 acetylation to many of their targets. Importantly, bioinformatic analysis of the sequences bound by each transcription factor (TF) shows an over-representation of motifs highly similar to the in vitro established consensus sequences. On the basis of these data, we have inferred tentative binding sites at base pair resolution. Some of these sites have been previously found by in vitro analysis and some were verified in vitro in this study. Our data suggests that a similar approach could be used for the in vivo characterization of all predicted/uncharacterized TF and that the analysis could be scaled to the whole genome.
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| 22. |
- Trunschke, Annette, et al.
(author)
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Towards Experimental Handbooks in Catalysis
- 2020
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In: Topics in Catalysis. - : Springer Science and Business Media LLC. - 1572-9028 .- 1022-5528. ; 63:19-20, s. 1683-1699
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Journal article (peer-reviewed)abstract
- The “Seven Pillars” of oxidation catalysis proposed by Robert K. Grasselli represent an early example of phenomenological descriptors in the field of heterogeneous catalysis. Major advances in the theoretical description of catalytic reactions have been achieved in recent years and new catalysts are predicted today by using computational methods. To tackle the immense complexity of high-performance systems in reactions where selectivity is a major issue, analysis of scientific data by artificial intelligence and data science provides new opportunities for achieving improved understanding. Modern data analytics require data of highest quality and sufficient diversity. Existing data, however, frequently do not comply with these constraints. Therefore, new concepts of data generation and management are needed. Herein we present a basic approach in defining best practice procedures of measuring consistent data sets in heterogeneous catalysis using “handbooks”. Selective oxidation of short-chain alkanes over mixed metal oxide catalysts was selected as an example.
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