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1.	Alexander, Stephen P. H., et al. (författare) The Concise Guide to PHARMACOLOGY 2023/24: G protein-coupled receptors 2023 Ingår i: BRITISH JOURNAL OF PHARMACOLOGY. - : British pharmacological society. - 0007-1188 .- 1476-5381. ; 180 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.
2.	Christopoulos, Arthur, et al. (författare) THE CONCISE GUIDE TO PHARMACOLOGY 2021/22: G protein-coupled receptors. 2021 Ingår i: British journal of pharmacology. - : Wiley. - 1476-5381 .- 0007-1188. ; 178 Suppl 1 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.
3.	Rodriguez, Sébastien, et al. (författare) Science goals and new mission concepts for future exploration of Titan's atmosphere, geology and habitability : titan POlar scout/orbitEr and in situ lake lander and DrONe explorer (POSEIDON) 2022 Ingår i: Experimental astronomy. - : Springer Science and Business Media LLC. - 0922-6435 .- 1572-9508. ; 54:2-3, s. 911-973 Tidskriftsartikel (refereegranskat)abstract In response to ESA’s “Voyage 2050” announcement of opportunity, we propose an ambitious L-class mission to explore one of the most exciting bodies in the Solar System, Saturn’s largest moon Titan. Titan, a “world with two oceans”, is an organic-rich body with interior-surface-atmosphere interactions that are comparable in complexity to the Earth. Titan is also one of the few places in the Solar System with habitability potential. Titan’s remarkable nature was only partly revealed by the Cassini-Huygens mission and still holds mysteries requiring a complete exploration using a variety of vehicles and instruments. The proposed mission concept POSEIDON (Titan POlar Scout/orbitEr and In situ lake lander DrONe explorer) would perform joint orbital and in situ investigations of Titan. It is designed to build on and exceed the scope and scientific/technological accomplishments of Cassini-Huygens, exploring Titan in ways that were not previously possible, in particular through full close-up and in situ coverage over long periods of time. In the proposed mission architecture, POSEIDON consists of two major elements: a spacecraft with a large set of instruments that would orbit Titan, preferably in a low-eccentricity polar orbit, and a suite of in situ investigation components, i.e. a lake lander, a “heavy” drone (possibly amphibious) and/or a fleet of mini-drones, dedicated to the exploration of the polar regions. The ideal arrival time at Titan would be slightly before the next northern Spring equinox (2039), as equinoxes are the most active periods to monitor still largely unknown atmospheric and surface seasonal changes. The exploration of Titan’s northern latitudes with an orbiter and in situ element(s) would be highly complementary in terms of timing (with possible mission timing overlap), locations, and science goals with the upcoming NASA New Frontiers Dragonfly mission that will provide in situ exploration of Titan’s equatorial regions, in the mid-2030s.
4.	Scheuermann, Fabian, et al. (författare) Stellar associations powering H ii regions - I. Defining an evolutionary sequence 2023 Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 522:2, s. 2369-2383 Tidskriftsartikel (refereegranskat)abstract Connecting the gas in H II regions to the underlying source of the ionizing radiation can help us constrain the physical processes of stellar feedback and how H II regions evolve over time. With PHANGS-MUSE, we detect nearly 24 000 H II regions across 19 galaxies and measure the physical properties of the ionized gas (e.g. metallicity, ionization parameter, and density). We use catalogues of multiscale stellar associations from PHANGS-HST to obtain constraints on the age of the ionizing sources. We construct a matched catalogue of 4177 H II regions that are clearly linked to a single ionizing association. A weak anticorrelation is observed between the association ages and the H a equi v alent width EW (H a), the H a/ FUV flux ratio, and the ionization parameter, log q . As all three are expected to decrease as the stellar population ages, this could indicate that we observe an evolutionary sequence. This interpretation is further supported by correlations between all three properties. Interpreting these as evolutionary tracers, we find younger nebulae to be more attenuated by dust and closer to giant molecular clouds, in line with recent models of feedback-regulated star formation. We also observe strong correlations with the local metallicity variations and all three proposed age tracers, suggestive of star formation preferentially occurring in locations of locally enhanced metallicity. Overall, EW (H a) and log q show the most consistent trends and appear to be most reliable tracers for the age of an H II region.
5.	Thilker, David A., et al. (författare) PHANGS–JWST First Results : The Dust Filament Network of NGC 628 and Its Relation to Star Formation Activity 2023 Ingår i: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8205 .- 2041-8213. ; 944:2 Tidskriftsartikel (refereegranskat)abstract PHANGS–JWST mid-infrared (MIR) imaging of nearby spiral galaxies has revealed ubiquitous filaments of dust emission in intricate detail. We present a pilot study to systematically map the dust filament network (DFN) at multiple scales between 25 and 400 pc in NGC 628. MIRI images at 7.7, 10, 11.3, and 21 μm of NGC 628 are used to generate maps of the filaments in emission, while PHANGS–HST B-band imaging yields maps of dust attenuation features. We quantify the correspondence between filaments traced by MIR thermal continuum/polycyclic aromatic hydrocarbon (PAH) emission and filaments detected via extinction/scattering of visible light; the fraction of MIR flux contained in the DFN; and the fraction of H ii regions, young star clusters, and associations within the DFN. We examine the dependence of these quantities on the physical scale at which the DFN is extracted. With our highest-resolution DFN maps (25 pc filament width), we find that filaments in emission and attenuation are cospatial in 40% of sight lines, often exhibiting detailed morphological agreement; that ∼30% of the MIR flux is associated with the DFN; and that 75%–80% of the star formation in H ii regions and 60% of the mass in star clusters younger than 5 Myr are contained within the DFN. However, the DFN at this scale is anticorrelated with looser associations of stars younger than 5 Myr identified using PHANGS–HST near-UV imaging. We discuss the impact of these findings on studies of star formation and the interstellar medium, and the broad range of new investigations enabled by multiscale maps of the DFN.
6.	Chan, Kai M. A., et al. (författare) Levers and leverage points for pathways to sustainability 2020 Ingår i: People and Nature. - : Wiley. - 2575-8314. ; 2:3, s. 693-717 Tidskriftsartikel (refereegranskat)abstract 1. Humanity is on a deeply unsustainable trajectory. We are exceeding planetary boundaries and unlikely to meet many international sustainable development goals and global environmental targets. Until recently, there was no broadly accepted framework of interventions that could ignite the transformations needed to achieve these desired targets and goals.2. As a component of the IPBES Global Assessment, we conducted an iterative expert deliberation process with an extensive review of scenarios and pathways to sustainability, including the broader literature on indirect drivers, social change and sustainability transformation. We asked, what are the most important elements of pathways to sustainability?3. Applying a social-ecological systems lens, we identified eight priority points for intervention (leverage points) and five overarching strategic actions and priority interventions (levers), which appear to be key to societal transformation. The eight leverage points are: (1) Visions of a good life, (2) Total consumption and waste, (3) Latent values of responsibility, (4) Inequalities, (5) Justice and inclusion in conservation, (6) Externalities from trade and other telecouplings, (7) Responsible technology, innovation and investment, and (8) Education and knowledge generation and sharing. The five intertwined levers can be applied across the eight leverage points and more broadly. These include: (A) Incentives and capacity building, (B) Coordination across sectors and jurisdictions, (C) Pre-emptive action, (D) Adaptive decision-making and (E) Environmental law and implementation. The levers and leverage points are all non-substitutable, and each enables others, likely leading to synergistic benefits.4. Transformative change towards sustainable pathways requires more than a simple scaling-up of sustainability initiatives-it entails addressing these levers and leverage points to change the fabric of legal, political, economic and other social systems. These levers and leverage points build upon those approved within the Global Assessment's Summary for Policymakers, with the aim of enabling leaders in government, business, civil society and academia to spark transformative changes towards a more just and sustainable world.
7.	Hannon, Stephen, et al. (författare) Star cluster classification using deep transfer learning with PHANGS-HST 2023 Ingår i: Monthly notices of the Royal Astronomical Society. - 0035-8711 .- 1365-2966. ; 526:2, s. 2991-3006 Tidskriftsartikel (refereegranskat)abstract Currently available star cluster catalogues from the Hubble Space Telescope (HST) imaging of nearby galaxies heavily rely on visual inspection and classification of candidate clusters. The time-consuming nature of this process has limited the production of reliable catalogues and thus also post-observation analysis. To address this problem, deep transfer learning has recently been used to create neural network models that accurately classify star cluster morphologies at production scale for nearby spiral galaxies (D ≲ 20 Mpc). Here, we use HST ultraviolet (UV)–optical imaging of over 20 000 sources in 23 galaxies from the Physics at High Angular resolution in Nearby GalaxieS (PHANGS) survey to train and evaluate two new sets of models: (i) distance-dependent models, based on cluster candidates binned by galaxy distance (9–12, 14–18, and 18–24 Mpc), and (ii) distance-independent models, based on the combined sample of candidates from all galaxies. We find that the overall accuracy of both sets of models is comparable to previous automated star cluster classification studies (∼60–80 per cent) and shows improvement by a factor of 2 in classifying asymmetric and multipeaked clusters from PHANGS-HST. Somewhat surprisingly, while we observe a weak negative correlation between model accuracy and galactic distance, we find that training separate models for the three distance bins does not significantly improve classification accuracy. We also evaluate model accuracy as a function of cluster properties such as brightness, colour, and spectral energy distribution (SED)-fit age. Based on the success of these experiments, our models will provide classifications for the full set of PHANGS-HST candidate clusters (N ∼ 200 000) for public release.
8.	Kamal, Nadia, et al. (författare) The mosaic oat genome gives insights into a uniquely healthy cereal crop 2022 Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 606:7912, s. 113-119 Tidskriftsartikel (refereegranskat)abstract Cultivated oat (Avena sativa L.) is an allohexaploid (AACCDD, 2n = 6x = 42) thought to have been domesticated more than 3,000 years ago while growing as a weed in wheat, emmer and barley fields in Anatolia1,2. Oat has a low carbon footprint, substantial health benefits and the potential to replace animal-based food products. However, the lack of a fully annotated reference genome has hampered efforts to deconvolute its complex evolutionary history and functional gene dynamics. Here we present a high-quality reference genome of A. sativa and close relatives of its diploid (Avena longiglumis, AA, 2n = 14) and tetraploid (Avena insularis, CCDD, 2n = 4x = 28) progenitors. We reveal the mosaic structure of the oat genome, trace large-scale genomic reorganizations in the polyploidization history of oat and illustrate a breeding barrier associated with the genome architecture of oat. We showcase detailed analyses of gene families implicated in human health and nutrition, which adds to the evidence supporting oat safety in gluten-free diets, and we perform mapping-by-sequencing of an agronomic trait related to water-use efficiency. This resource for the Avena genus will help to leverage knowledge from other cereal genomes, improve understanding of basic oat biology and accelerate genomics-assisted breeding and reanalysis of quantitative trait studies.
9.	Kuhn, Jens H., et al. (författare) Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota) 2023 Ingår i: Journal of General Virology. - : Microbiology Society. - 0022-1317 .- 1465-2099. ; 104:8 Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract In April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
10.	Liu, Daizhong, et al. (författare) PHANGS–JWST First Results : Stellar-feedback-driven Excitation and Dissociation of Molecular Gas in the Starburst Ring of NGC 1365? 2023 Ingår i: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8205 .- 2041-8213. ; 944:2 Tidskriftsartikel (refereegranskat)abstract We compare embedded young massive star clusters (YMCs) to (sub-)millimeter line observations tracing the excitation and dissociation of molecular gas in the starburst ring of NGC 1365. This galaxy hosts one of the strongest nuclear starbursts and richest populations of YMCs within 20 Mpc. Here we combine near-/mid-IR PHANGS–JWST imaging with new Atacama Large Millimeter/submillimeter Array multi-J CO (1–0, 2–1 and 4–3) and [C ı] (1–0) mapping, which we use to trace CO excitation via R42 = ICO(4−3)/ICO(2−1) and R21 = ICO(2−1)/ICO(1−0) and dissociation via RCICO = I[CI](1−0)/ICO(2−1) at 330 pc resolution. We find that the gas flowing into the starburst ring from northeast to southwest appears strongly affected by stellar feedback, showing decreased excitation (lower R42) and increased signatures of dissociation (higher RCICO) in the downstream regions. There, radiative-transfer modeling suggests that the molecular gas density decreases and temperature and [CI/CO] abundance ratio increase. We compare R42 and RCICO with local conditions across the regions and find that both correlate with near-IR 2 μm emission tracing the YMCs and with both polycyclic aromatic hydrocarbon (11.3 μm) and dust continuum (21 μm) emission. In general, RCICO exhibits ∼0.1 dex tighter correlations than R42, suggesting C ı to be a more sensitive tracer of changing physical conditions in the NGC 1365 starburst than CO (4–3). Our results are consistent with a scenario where gas flows into the two arm regions along the bar, becomes condensed/shocked, forms YMCs, and then these YMCs heat and dissociate the gas.
11.	Peiffer, C., et al. (författare) On the equivalence of the X-ray scattering retrieval with beam tracking and analyser-based imaging using a synchrotron source 2023 Ingår i: Journal of Physics D. - : IOP Publishing. - 0022-3727 .- 1361-6463. ; 56:45 Tidskriftsartikel (refereegranskat)abstract X-ray phase contrast imaging (XPCI) methods give access to contrast mechanisms that are based on the refractive properties of matter on top of the absorption coefficient in conventional x-ray imaging. Ultra small angle x-ray scattering (USAXS) is a phase contrast mechanism that arises due to multiple refraction events caused by physical features of a scale below the physical resolution of the used imaging system. USAXS contrast can therefore give insight into subresolution structural information, which is an ongoing research topic in the vast field of different XPCI techniques. In this study, we quantitatively compare the USAXS signal retrieved by the beam tracking XPCI technique with the gold standard of the analyzer based imaging XPCI technique using a synchrotron x-ray source. We find that, provided certain conditions are met, the two methods measure the same quantity.
12.	Rodríguez, M. Jimena, et al. (författare) PHANGS–JWST First Results : Dust-embedded Star Clusters in NGC 7496 Selected via 3.3 μm PAH Emission 2023 Ingår i: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8205 .- 2041-8213. ; 944:2 Tidskriftsartikel (refereegranskat)abstract The earliest stages of star formation occur enshrouded in dust and are not observable in the optical. Here we leverage the extraordinary new high-resolution infrared imaging from JWST to begin the study of dust-embedded star clusters in nearby galaxies throughout the Local Volume. We present a technique for identifying dust-embedded clusters in NGC 7496 (18.7 Mpc), the first galaxy to be observed by the PHANGS–JWST Cycle 1 Treasury Survey. We select sources that have strong 3.3 μm PAH emission based on a F300M − F335M color excess and identify 67 candidate embedded clusters. Only eight of these are found in the PHANGS-HST optically selected cluster catalog, and all are young (six have SED fit ages of ∼1 Myr). We find that this sample of embedded cluster candidates may significantly increase the census of young clusters in NGC 7496 from the PHANGS-HST catalog; the number of clusters younger than ∼2 Myr could be increased by a factor of 2. Candidates are preferentially located in dust lanes and are coincident with the peaks in the PHANGS-ALMA CO (2–1) maps. We take a first look at concentration indices, luminosity functions, SEDs spanning from 2700 Å to 21 μm, and stellar masses (estimated to be between ∼104 and 105 M⊙). The methods tested here provide a basis for future work to derive accurate constraints on the physical properties of embedded clusters, characterize the completeness of cluster samples, and expand analysis to all 19 galaxies in the PHANGS–JWST sample, which will enable basic unsolved problems in star formation and cluster evolution to be addressed.
13.	Thurner, Lorenz, et al. (författare) Lymphocyte predominant cells detect Moraxella catarrhalis-derived antigens in nodular lymphocyte-predominant Hodgkin lymphoma 2020 Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 11:1 Tidskriftsartikel (refereegranskat)abstract Nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) is a rare lymphoma of B-cell origin with frequent expression of functional B-cell receptors (BCRs). Here we report that expression cloning followed by antigen screening identifies DNA-directed RNA polymerase beta' (RpoC) from Moraxella catarrhalis as frequent antigen of BCRs of IgD(+) LP cells. Patients show predominance of HLA-DRB1*04/07 and the IgVH genes encode extraordinarily long CDR3s. High-titer, light-chain-restricted anti-RpoC IgG1/kappa -type serum-antibodies are additionally found in these patients. RpoC and MID/hag, a superantigen co-expressed by Moraxella catarrhalis that is known to activate IgD(+) B cells by binding to the Fc domain of IgD, have additive activation effects on the BCR, the NF-kappa B pathway and the proliferation of IgD(+) DEV cells expressing RpoC-specific BCRs. This suggests an additive antigenic and superantigenic stimulation of B cells with RpoC-specific IgD(+) BCRs under conditions of a permissive MHC-II haplotype as a model of NLPHL lymphomagenesis, implying future treatment strategies. Nodular lymphocyte-predominant Hodgkin lymphoma with IgD+ lymphocyte-predominant (LP) cells is a rare clinical distinct lymphoma subset of B-cell origin. Here the authors show that antigens expressed by Moraxella catarrhalis are recognized by B cell receptors of IgD+ LP cells, suggesting the contribution of chronic antigen stimulation to lymphomagenesis.
14.	Ebinghaus, Ralf, et al. (författare) Berlin statement on legacy and emerging contaminants in polar regions 2023 Ingår i: Chemosphere. - : Elsevier BV. - 0045-6535 .- 1879-1298. ; 327 Tidskriftsartikel (refereegranskat)abstract Polar regions should be given greater consideration with respect to the monitoring, risk assessment, and management of potentially harmful chemicals, consistent with requirements of the precautionary principle. Protecting the vulnerable polar environments requires (i) raising political and public awareness and (ii) restricting and preventing global emissions of harmful chemicals at their sources. The Berlin Statement is the outcome of an international workshop with representatives of the European Commission, the Arctic Council, the Antarctic Treaty Consultative Meeting, the Stockholm Convention on Persistent Organic Pollutants (POPs), environmental specimen banks, and data centers, as well as scientists from various international research institutions. The statement addresses urgent chemical pollution issues in the polar regions and provides recommendations for improving screening, monitoring, risk assessment, research cooperation, and open data sharing to provide environmental policy makers and chemicals management decision-makers with relevant and reliable contaminant data to better protect the polar environments. The consensus reached at the workshop can be summarized in just two words: “Act now!”Specifically, “Act now!” to reduce the presence and impact of anthropogenic chemical pollution in polar regions by.•Establishing participatory co-development frameworks in a permanent multi-disciplinary platform for Arctic-Antarctic collaborations and establishing exchanges between the Arctic Monitoring and Assessment Program (AMAP) of the Arctic Council and the Antarctic Monitoring and Assessment Program (AnMAP) of the Scientific Committee on Antarctic Research (SCAR) to increase the visibility and exchange of contaminant data and to support the development of harmonized monitoring programs.•Integrating environmental specimen banking, innovative screening approaches and archiving systems, to provide opportunities for improved assessment of contaminants to protect polar regions.
15.	Flechard, Chris R., et al. (författare) Carbon-nitrogen interactions in European forests and semi-natural vegetation - Part 1: Fluxes and budgets of carbon, nitrogen and greenhouse gases from ecosystem monitoring and modelling 2020 Ingår i: Biogeosciences. - : Copernicus GmbH. - 1726-4170 .- 1726-4189. ; 17:6, s. 1583-1620 Tidskriftsartikel (refereegranskat)abstract The impact of atmospheric reactive nitrogen (N-r) deposition on carbon (C) sequestration in soils and biomass of unfertilized, natural, semi-natural and forest ecosystems has been much debated. Many previous results of this dC/dN response were based on changes in carbon stocks from periodical soil and ecosystem inventories, associated with estimates of N-r deposition obtained from large-scale chemical transport models. This study and a companion paper (Flechard et al., 2020) strive to reduce uncertainties of N effects on C sequestration by linking multi-annual gross and net ecosystem productivity estimates from 40 eddy covariance flux towers across Europe to local measurement-based estimates of dry and wet N-r deposition from a dedicated collocated monitoring network. To identify possible ecological drivers and processes affecting the interplay between C and N-r inputs and losses, these data were also combined with in situ flux measurements of NO, N2O and CH4 fluxes; soil NO3- leaching sampling; and results of soil incubation experiments for N and greenhouse gas (GHG) emissions, as well as surveys of available data from online databases and from the literature, together with forest ecosystem (BAS-FOR) modelling. Multi-year averages of net ecosystem productivity (NEP) in forests ranged from -70 to 826 gCm(-2) yr(-1) at total wet + dry inorganic N-r deposition rates (N-dep) of 0.3 to 4.3 gNm(-2) yr(-1) and from -4 to 361 g Cm-2 yr(-1) at N-dep rates of 0.1 to 3.1 gNm(-2) yr(-1) in short semi-natural vegetation (moorlands, wetlands and unfertilized extensively managed grasslands). The GHG budgets of the forests were strongly dominated by CO2 exchange, while CH4 and N2O exchange comprised a larger proportion of the GHG balance in short semi-natural vegetation. Uncertainties in elemental budgets were much larger for nitrogen than carbon, especially at sites with elevated N-dep where N-r leaching losses were also very large, and compounded by the lack of reliable data on organic nitrogen and N-2 losses by denitrification. Nitrogen losses in the form of NO, N2O and especially NO3- were on average 27%(range 6 %-54 %) of N-dep at sites with N-dep < 1 gNm(-2) yr(-1) versus 65% (range 35 %-85 %) for N-dep > 3 gNm(-2) yr(-1). Such large levels of N-r loss likely indicate that different stages of N saturation occurred at a number of sites. The joint analysis of the C and N budgets provided further hints that N saturation could be detected in altered patterns of forest growth. Net ecosystem productivity increased with N-r deposition up to 2-2.5 gNm(-2) yr(-1), with large scatter associated with a wide range in carbon sequestration efficiency (CSE, defined as the NEP/GPP ratio). At elevated N-dep levels (> 2.5 gNm(-2) yr(-1)), where inorganic N-r losses were also increasingly large, NEP levelled off and then decreased. The apparent increase in NEP at low to intermediate N-dep levels was partly the result of geographical cross-correlations between N-dep and climate, indicating that the actual mean dC/dN response at individual sites was significantly lower than would be suggested by a simple, straightforward regression of NEP vs. N-dep.
16.	Haugg, Amelie, et al. (författare) Predictors of real-time fMRI neurofeedback performance and improvement - A machine learning mega-analysis. 2021 Ingår i: NeuroImage. - : Elsevier. - 1053-8119 .- 1095-9572. ; 237 Tidskriftsartikel (refereegranskat)abstract Real-time fMRI neurofeedback is an increasingly popular neuroimaging technique that allows an individual to gain control over his/her own brain signals, which can lead to improvements in behavior in healthy participants as well as to improvements of clinical symptoms in patient populations. However, a considerably large ratio of participants undergoing neurofeedback training do not learn to control their own brain signals and, consequently, do not benefit from neurofeedback interventions, which limits clinical efficacy of neurofeedback interventions. As neurofeedback success varies between studies and participants, it is important to identify factors that might influence neurofeedback success. Here, for the first time, we employed a big data machine learning approach to investigate the influence of 20 different design-specific (e.g. activity vs. connectivity feedback), region of interest-specific (e.g. cortical vs. subcortical) and subject-specific factors (e.g. age) on neurofeedback performance and improvement in 608 participants from 28 independent experiments. With a classification accuracy of 60% (considerably different from chance level), we identified two factors that significantly influenced neurofeedback performance: Both the inclusion of a pre-training no-feedback run before neurofeedback training and neurofeedback training of patients as compared to healthy participants were associated with better neurofeedback performance. The positive effect of pre-training no-feedback runs on neurofeedback performance might be due to the familiarization of participants with the neurofeedback setup and the mental imagery task before neurofeedback training runs. Better performance of patients as compared to healthy participants might be driven by higher motivation of patients, higher ranges for the regulation of dysfunctional brain signals, or a more extensive piloting of clinical experimental paradigms. Due to the large heterogeneity of our dataset, these findings likely generalize across neurofeedback studies, thus providing guidance for designing more efficient neurofeedback studies specifically for improving clinical neurofeedback-based interventions. To facilitate the development of data-driven recommendations for specific design details and subpopulations the field would benefit from stronger engagement in open science research practices and data sharing.
17.	Laj, Paolo, et al. (författare) A global analysis of climate-relevant aerosol properties retrieved from the network of Global Atmosphere Watch (GAW) near-surface observatories 2020 Ingår i: Atmospheric Measurement Techniques. - : Copernicus GmbH. - 1867-1381 .- 1867-8548. ; 13:8, s. 4353-4392 Tidskriftsartikel (refereegranskat)abstract Aerosol particles are essential constituents of the Earth's atmosphere, impacting the earth radiation balance directly by scattering and absorbing solar radiation, and indirectly by acting as cloud condensation nuclei. In contrast to most greenhouse gases, aerosol particles have short atmospheric residence times, resulting in a highly heterogeneous distribution in space and time. There is a clear need to document this variability at regional scale through observations involving, in particular, the in situ near-surface segment of the atmospheric observation system. This paper will provide the widest effort so far to document variability of climate-relevant in situ aerosol properties (namely wavelength dependent particle light scattering and absorption coefficients, particle number concentration and particle number size distribution) from all sites connected to the Global Atmosphere Watch network. High-quality data from almost 90 stations worldwide have been collected and controlled for quality and are reported for a reference year in 2017, providing a very extended and robust view of the variability of these variables worldwide. The range of variability observed worldwide for light scattering and absorption coefficients, single-scattering albedo, and particle number concentration are presented together with preliminary information on their long-term trends and comparison with model simulation for the different stations. The scope of the present paper is also to provide the necessary suite of information, including data provision procedures, quality control and analysis, data policy, and usage of the ground-based aerosol measurement network. It delivers to users of the World Data Centre on Aerosol, the required confidence in data products in the form of a fully characterized value chain, including uncertainty estimation and requirements for contributing to the global climate monitoring system.
18.	Larson, Kirsten L., et al. (författare) Multiscale stellar associations across the star formation hierarchy in PHANGS-HST nearby galaxies : methodology and properties 2023 Ingår i: Monthly notices of the Royal Astronomical Society. - 0035-8711 .- 1365-2966. ; 523:4, s. 6061-6081 Tidskriftsartikel (refereegranskat)abstract We develop a method to identify and determine the physical properties of stellar associations using Hubble Space Telescope (HST) NUV−U−B−V−I imaging of nearby galaxies from the Physics at High Angular Resolution in Nearby GalaxieS with the Hubble Space Telescope (PHANGS–HST) survey. We apply a watershed algorithm to density maps constructed from point source catalogues Gaussian smoothed to multiple physical scales from 8 to 64 pc. We develop our method on two galaxies that span the distance range in the PHANGS–HST sample: NGC 3351 (10 Mpc) and NGC 1566 (18 Mpc). We test our algorithm with different parameters such as the choice of detection band for the point source catalogue (NUV or V), source density image filtering methods, and absolute magnitude limits. We characterize the properties of the resulting multiscale associations, including sizes, number of tracer stars, number of associations, and photometry, as well as ages, masses, and reddening from spectral energy distribution fitting. Our method successfully identifies structures that occupy loci in the UBVI colour–colour diagram consistent with previously published catalogues of clusters and associations. The median ages of the associations increase from log(age/yr) = 6.6 to log(age/yr) = 6.9 as the spatial scale increases from 8 to 64 pc for both galaxies. We find that the youngest stellar associations, with ages <3 Myr, indeed closely trace H II regions in H α imaging, and that older associations are increasingly anticorrelated with the H α emission. Owing to our new method, the PHANGS–HST multiscale associations provide a far more complete census of recent star formation activity than found with previous cluster and compact association catalogues.
19.	Lossow, Stefan, 1977, et al. (författare) A reassessment of the discrepancies in the annual variation of δD-H2O in the tropical lower stratosphere between the MIPAS and ACE-FTS satellite data sets 2020 Ingår i: Atmospheric Measurement Techniques. - : Copernicus GmbH. - 1867-1381 .- 1867-8548. ; 13:1, s. 287-308 Tidskriftsartikel (refereegranskat)abstract The annual variation of δD in the tropical lower stratosphere is a critical indicator for the relative importance of different processes contributing to the transport of water vapour through the cold tropical tropopause region into the stratosphere. Distinct observational discrepancies of the δD annual variation were visible in the works of Steinwagner et al. (2010) and Randel et al. (2012). Steinwagner et al. (2010) analysed MIPAS (Michelson Interferometer for Passive Atmospheric Sounding) observations retrieved with the IMK/IAA (Institut für Meteorologie und Klimaforschung in Karlsruhe, Germany, in collaboration with the Instituto de Astrofísica de Andalucía in Granada, Spain) processor, while Randel et al. (2012) focused on ACE-FTS (Atmospheric Chemistry Experiment Fourier Transform Spectrometer) observations. Here we reassess the discrepancies based on newer MIPAS (IMK/IAA) and ACE-FTS data sets, also showing for completeness results from SMR (Sub-Millimetre Radiometer) observations and a ECHAM/MESSy (European Centre for Medium-Range Weather Forecasts Hamburg and Modular Earth Submodel System) Atmospheric Chemistry (EMAC) simulation (Eichinger et al., 2015b). Similar to the old analyses, the MIPAS data set yields a pronounced annual variation (maximum about 75 ‰), while that derived from the ACE-FTS data set is rather weak (maximum about 25 ‰). While all data sets exhibit the phase progression typical for the tape recorder, the annual maximum in the ACE-FTS data set precedes that in the MIPAS data set by 2 to 3 months. We critically consider several possible reasons for the observed discrepancies, focusing primarily on the MIPAS data set. We show that the δD annual variation in the MIPAS data up to an altitude of 40 hPa is substantially impacted by a “start altitude effect”, i.e. dependency between the lowermost altitude where MIPAS retrievals are possible and retrieved data at higher altitudes. In itself this effect does not explain the differences with the ACE-FTS data. In addition, there is a mismatch in the vertical resolution of the MIPAS HDO and H2O data (being consistently better for HDO), which actually results in an artificial tape-recorder-like signal in δD. Considering these MIPAS characteristics largely removes any discrepancies between the MIPAS and ACE-FTS data sets and shows that the MIPAS data are consistent with a δD tape recorder signal with an amplitude of about 25 ‰ in the lowermost stratosphere.
20.	Maasri, Alain, et al. (författare) A global agenda for advancing freshwater biodiversity research 2022 Ingår i: Ecology Letters. - : Wiley. - 1461-023X .- 1461-0248. ; 25:2, s. 255-263 Tidskriftsartikel (refereegranskat)abstract Global freshwater biodiversity is declining dramatically, and meeting the challenges of this crisis requires bold goals and the mobilisation of substantial resources. While the reasons are varied, investments in both research and conservation of freshwater biodiversity lag far behind those in the terrestrial and marine realms. Inspired by a global consultation, we identify 15 pressing priority needs, grouped into five research areas, in an effort to support informed stewardship of freshwater biodiversity. The proposed agenda aims to advance freshwater biodiversity research globally as a critical step in improving coordinated actions towards its sustainable management and conservation.
21.	Aggestam, Karin, et al. (författare) Gender and Peaceful Change 2021 Ingår i: The Oxford Handbook of Peaceful Change in International Relations. - : Oxford University Press. Bokkapitel (refereegranskat)abstract This chapter examines the interplay between gender and peaceful change. It elaborates on how the concept of peace is inherently gendered by drawing upon feminist scholarship. There are a number of ways to conceptualize gender and peaceful change. The “women-peace hypothesis” assumes a proximity between women’s peacefulness and their experiences of maternal care. However, such a construction needs to be treated with caution since transformative peace requires deconstruction of that assumption, while staying attentive to women’s contributions to peacemaking. Debates on strategic essentialism and inclusive peace are also assessed as a way of gaining deeper and more meaningful understandings of gender-just peaceful change. We argue that women’s unique experiences pertaining to peace and conflict should be considered alongside those of men. In addition, we examine the assumption about states with a poor record on gender inequality are more likely to be involved in intrastate conflicts. The last part of the chapter focuses on policy practice, including the adoption of UNSCR 1325 on Women, Peace, and Security and the reorientation in some states toward feminist foreign policy as a platform for peaceful change.
22.	Ahmadi, Delaram, et al. (författare) Nanoscale Structure and Dynamics of Model Membrane Lipid Raft Systems, Studied by Neutron Scattering Methods 2022 Ingår i: Frontiers in Physics. - : Frontiers Media SA. - 2296-424X. ; 10 Tidskriftsartikel (refereegranskat)abstract Quasi-elastic neutron scattering (QENS) and small angle neutron scattering (SANS), in combination with isotopic contrast variation, have been used to determine the structure and dynamics of three-component lipid membranes, in the form of vesicles, comprising an unsaturated [palmitoyl-oleoyl-phosphatidylcholine (POPC) or dioleoyl-phosphatidylcholine (DOPC)], a saturated phospholipid (dipalmitoyl-phosphatidylcholine (DPPC)), and cholesterol, as a function temperature and composition. SANS studies showed vesicle membranes composed of a 1:1:1 molar ratio of DPPC:DOPC:cholesterol and a 2:2:1 molar ratio of DPPC:POPC:cholesterol phase separated, forming lipid rafts of ∼18 and ∼7 nm diameter respectively, when decreasing temperature from 308 to 297 K. Phase separation was reversible upon increasing temperature. The larger rafts observed in systems containing DOPC are attributed to the greater mis-match in lipid alkyl chains between DOPC and DPPC, than for POPC and DPPC. QENS studies, over the temperature range 283–323K, showed that the resulting data were best modelled by two Lorentzian functions: a narrow component, describing the “in-plane” lipid diffusion, and a broader component, describing the lipid alkyl chain segmental relaxation. The overall “in-plane” diffusion was found to show a significant reduction upon increasing temperature due to the vesicle membranes transitioning from one containing rafts to one where the component lipids are homogeneously mixed. The use of different isotopic combinations allowed the measured overall reduction of in-plane diffusion to be understood in terms of an increase in diffusion of the saturated DPPC lipid and a corresponding decrease in diffusion of the unsaturated DOPC/POPC lipid. As the rafts are considered to be composed principally of saturated lipid and cholesterol, the breakdown of rafts decreases the exposure of the DPPC to cholesterol whilst increasing the exposure of cholesterol to unsaturated lipid. These results show the sensitivity of lipid diffusion to local cholesterol concentration, and the importance of considering the local, rather that the global composition of a membrane when understanding the diffusion processes of lipids within the membrane. The novel combination of SANS and QENS allows a non-intrusive approach to characterize the structure and dynamics occurring in phase-separated model membranes which are designed to mimic the lateral heterogeneity of lipids seen in cellular membranes–a heterogeneity that can have pathological consequences.
23.	Alexandridis, Nikolaos, et al. (författare) Archetype models upscale understanding of natural pest control response to land-use change 2022 Ingår i: Ecological Applications. - : Wiley. - 1051-0761 .- 1939-5582. ; 32:8 Tidskriftsartikel (refereegranskat)abstract Control of crop pests by shifting host plant availability and natural enemy activity at landscape scales has great potential to enhance the sustainability of agriculture. However, mainstreaming natural pest control requires improved understanding of how its benefits can be realized across a variety of agroecological contexts. Empirical studies suggest significant but highly variable responses of natural pest control to land-use change. Current ecological models are either too specific to provide insight across agroecosystems, or too generic to guide management with actionable predictions. We suggest getting the full benefit of available empirical, theoretical and methodological knowledge, by combining trait-mediated understanding from correlative studies with the explicit representation of causal relationships achieved by mechanistic modeling. To link these frameworks, we adapt the concept of archetypes, or context-specific generalizations, from sustainability science. Similar responses of natural pest control to land-use gradients across cases that share key attributes, such as functional traits of focal organisms, indicate general processes that drive system behavior in a context-sensitive manner. Based on such observations of natural pest control, a systematic definition of archetypes can provide the basis for mechanistic models of intermediate generality that cover all major agroecosystems worldwide. Example applications demonstrate the potential for upscaling understanding and improving prediction of natural pest control, based on knowledge transfer and scientific synthesis. A broader application of this mechanistic archetype approach promises to enhance ecology's contribution to natural resource management across diverse regions and social-ecological contexts.
24.	Alexandridis, Nikolaos, et al. (författare) Models of natural pest control : Towards predictions across agricultural landscapes 2021 Ingår i: Biological Control. - : Elsevier BV. - 1049-9644. ; 163 Forskningsöversikt (refereegranskat)abstract Natural control of invertebrate crop pests has the potential to complement or replace conventional insecticide-based practices, but its mainstream application is hampered by predictive unreliability across agroecosystems. Inconsistent responses of natural pest control to changes in landscape characteristics have been attributed to ecological complexity and system-specific conditions. Here, we review agroecological models and their potential to provide predictions of natural pest control across agricultural landscapes. Existing models have used a multitude of techniques to represent specific crop-pest-enemy systems at various spatiotemporal scales, but less wealthy regions of the world are underrepresented. A realistic representation of natural pest control across systems appears to be hindered by a practical trade-off between generality and realism. Nonetheless, observations of context-sensitive, trait-mediated responses of natural pest control to land-use gradients indicate the potential of ecological models that explicitly represent the underlying mechanisms. We conclude that modelling natural pest control across agroecosystems should exploit existing mechanistic techniques towards a framework of contextually bound generalizations. Observed similarities in causal relationships can inform the functional grouping of diverse agroecosystems worldwide and the development of the respective models based on general, but context-sensitive, ecological mechanisms. The combined use of qualitative and quantitative techniques should allow the flexible integration of empirical evidence and ecological theory for robust predictions of natural pest control across a wide range of agroecological contexts and levels of knowledge availability. We highlight challenges and promising directions towards developing such a general modelling framework.
25.	Amici, Julia, et al. (författare) A Roadmap for Transforming Research to Invent the Batteries of the Future Designed within the European Large Scale Research Initiative BATTERY 2030 2022 Ingår i: Advanced Energy Materials. - : John Wiley & Sons. - 1614-6832 .- 1614-6840. ; 12:17 Forskningsöversikt (refereegranskat)abstract This roadmap presents the transformational research ideas proposed by "BATTERY 2030+," the European large-scale research initiative for future battery chemistries. A "chemistry-neutral" roadmap to advance battery research, particularly at low technology readiness levels, is outlined, with a time horizon of more than ten years. The roadmap is centered around six themes: 1) accelerated materials discovery platform, 2) battery interface genome, with the integration of smart functionalities such as 3) sensing and 4) self-healing processes. Beyond chemistry related aspects also include crosscutting research regarding 5) manufacturability and 6) recyclability. This roadmap should be seen as an enabling complement to the global battery roadmaps which focus on expected ultrahigh battery performance, especially for the future of transport. Batteries are used in many applications and are considered to be one technology necessary to reach the climate goals. Currently the market is dominated by lithium-ion batteries, which perform well, but despite new generations coming in the near future, they will soon approach their performance limits. Without major breakthroughs, battery performance and production requirements will not be sufficient to enable the building of a climate-neutral society. Through this "chemistry neutral" approach a generic toolbox transforming the way batteries are developed, designed and manufactured, will be created.
26.	Badian, Reza A., et al. (författare) Wide-field mosaics of the corneal subbasal nerve plexus in Parkinsons disease using in vivo confocal microscopy 2021 Ingår i: Scientific Data. - : Nature Portfolio. - 2052-4463. ; 8:1 Tidskriftsartikel (refereegranskat)abstract In vivo confocal microscopy (IVCM) is a non-invasive imaging technique facilitating real-time acquisition of images from the live cornea and its layers with high resolution (1-2 mu m) and high magnification (600 to 800-fold). IVCM is extensively used to examine the cornea at a cellular level, including the subbasal nerve plexus (SBNP). IVCM of the cornea has thus gained intense interest for probing ophthalmic and systemic diseases affecting peripheral nerves. One of the main drawbacks, however, is the small field of view of IVCM, preventing an overview of SBNP architecture and necessitating subjective image sampling of small areas of the SBNP for analysis. Here, we provide a high-quality dataset of the corneal SBNP reconstructed by automated mosaicking, with an average mosaic image size corresponding to 48 individual IVCM fields of view. The mosaic dataset represents a group of 42 individuals with Parkinsons disease (PD) with and without concurrent restless leg syndrome. Additionally, mosaics from a control group (n = 13) without PD are also provided, along with clinical data for all included participants.
27.	Bott, Lukas Thomas, et al. (författare) Coulomb dissociation of O-16 into He-4 and C-12 2023 Ingår i: NUCLEAR PHYSICS IN ASTROPHYSICS - X, NPA-X 2022. - : EDP Sciences. - 2100-014X. ; 279 Konferensbidrag (refereegranskat)abstract We measured the Coulomb dissociation of O-16 into He-4 and C-12 within the FAIR Phase-0 program at GSI Helmholtzzentrum fur Schwerionenforschung Darmstadt, Germany. From this we will extract the photon dissociation cross section O-16(alpha,gamma)C-12, which is the time reversed reaction to C-12(alpha,gamma)O-16. With this indirect method, we aim to improve on the accuracy of the experimental data at lower energies than measured so far. The expected low cross section for the Coulomb dissociation reaction and close magnetic rigidity of beam and fragments demand a high precision measurement. Hence, new detector systems were built and radical changes to the (RB)-B-3 setup were necessary to cope with the high-intensity O-16 beam. All tracking detectors were designed to let the unreacted O-16 ions pass, while detecting the C-12 and He-4.
28.	Brander, Gustaf, et al. (författare) A population-based family clustering study of tic-related obsessive-compulsive disorder 2021 Ingår i: Molecular Psychiatry. - : Nature Publishing Group. - 1359-4184 .- 1476-5578. ; 26:4, s. 1224-1233 Tidskriftsartikel (refereegranskat)abstract In the latest edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5), obsessive-compulsive disorder (OCD) included a new "tic-related" specifier. However, strong evidence supporting tic-related OCD as a distinct subtype of OCD is lacking. This study investigated whether, at the population level, tic-related OCD has a stronger familial load than non-tic-related OCD. From a cohort of individuals born in Sweden between 1967 and 2007 (n = 4,085,367; 1257 with tic-related OCD and 20,975 with non-tic-related OCD), we identified all twins, full siblings, maternal and paternal half siblings, and cousins. Sex- and birth year-adjusted hazard ratios (aHR) were calculated to estimate the risk of OCD in relatives of individuals with OCD with and without comorbid tics, compared with relatives of unaffected individuals. We found that OCD is a familial disorder, regardless of comorbid tic disorder status. However, the risk of OCD in relatives of individuals with tic-related OCD was considerably greater than the risk of OCD in relatives of individuals with non-tic-related OCD (e.g., risk for full siblings: aHR = 10.63 [95% CI, 7.92-14.27] and aHR = 4.52 [95% CI, 4.06-5.02], respectively; p value for the difference < 0.0001). These differences remained when the groups were matched by age at first OCD diagnosis and after various sensitivity analyses. The observed familial patterns of OCD in relation to tics were not seen in relation to other neuropsychiatric comorbidities. Tic-related OCD is a particularly familial subtype of OCD. The results have important implications for ongoing gene-searching efforts.
29.	De Angelis, D., et al. (författare) A sub-100 nm thickness flat jet for extreme ultraviolet to soft X-ray absorption spectroscopy 2024 Ingår i: Journal of Synchrotron Radiation. - : International Union of Crystallography (IUCr). - 0909-0495 .- 1600-5775. ; 31:3 Pt, s. 605-612 Tidskriftsartikel (refereegranskat)abstract Experimental characterization of the structural, electronic and dynamic properties of dilute systems in aqueous solvents, such as nanoparticles, molecules and proteins, are nowadays an open challenge. X-ray absorption spectroscopy (XAS) is probably one of the most established approaches to this aim as it is element-specific. However, typical dilute systems of interest are often composed of light elements that require extreme-ultraviolet to soft X-ray photons. In this spectral regime, water and other solvents are rather opaque, thus demanding radical reduction of the solvent volume and removal of the liquid to minimize background absorption. Here, we present an experimental endstation designed to operate a liquid flat jet of sub-micrometre thickness in a vacuum environment compatible with extreme ultraviolet/soft XAS measurements in transmission geometry. The apparatus developed can be easily connected to synchrotron and free-electron-laser user-facility beamlines dedicated to XAS experiments. The conditions for stable generation and control of the liquid flat jet are analyzed and discussed. Preliminary soft XAS measurements on some test solutions are shown.
30.	Demichev, Vadim, et al. (författare) A time-resolved proteomic and prognostic map of COVID-19 2021 Ingår i: Cell Systems. - : Elsevier BV. - 2405-4712 .- 2405-4720. ; 12:8, s. 780-794.e7 Tidskriftsartikel (refereegranskat)abstract COVID-19 is highly variable in its clinical presentation, ranging from asymptomatic infection to severe organ damage and death. We characterized the time-dependent progression of the disease in 139 COVID-19 inpatients by measuring 86 accredited diagnostic parameters, such as blood cell counts and enzyme activities, as well as untargeted plasma proteomes at 687 sampling points. We report an initial spike in a systemic inflammatory response, which is gradually alleviated and followed by a protein signature indicative of tissue repair, metabolic reconstitution, and immunomodulation. We identify prognostic marker signatures for devising risk-adapted treatment strategies and use machine learning to classify therapeutic needs. We show that the machine learning models based on the proteome are transferable to an independent cohort. Our study presents a map linking routinely used clinical diagnostic parameters to plasma proteomes and their dynamics in an infectious disease.
31.	Dornelles, Andre Z., et al. (författare) Towards a bridging concept for undesirable resilience in social-ecological systems 2020 Ingår i: Global Sustainability. - : Cambridge University Press (CUP). - 2059-4798. ; 3 Tidskriftsartikel (refereegranskat)abstract Non-technical summary Resilience is a cross-disciplinary concept that is relevant for understanding the sustainability of the social and environmental conditions in which we live. Most research normatively focuses on building or strengthening resilience, despite growing recognition of the importance of breaking the resilience of, and thus transforming, unsustainable social-ecological systems. Undesirable resilience (cf. lock-ins, social-ecological traps), however, is not only less explored in the academic literature, but its understanding is also more fragmented across different disciplines. This disparity can inhibit collaboration among researchers exploring interdependent challenges in sustainability sciences. In this article, we propose that the term lock-in may contribute to a common understanding of undesirable resilience across scientific fields. Technical summary Resilience is an extendable concept that bridges the social and life sciences. Studies increasingly interpret resilience normatively as a desirable property of social-ecological systems, despite growing awareness of resilient properties leading to social and ecological degradation, vulnerability or barriers that hinder sustainability transformations (i.e., 'undesirable' resilience). This is the first study to qualify, quantify and compare the conceptualization of 'desirable' and 'undesirable' resilience across academic disciplines. Our literature analysis found that various synonyms are used to denote undesirable resilience (e.g., path dependency, social-ecological traps, institutional inertia). Compared to resilience as a desirable property, research on undesirable resilience is substantially less frequent and scattered across distinct scientific fields. Amongst synonyms for undesirable resilience, the term lock-in is more frequently and evenly used across academic disciplines. We propose that lock-in therefore has the potential to reconcile diverse interpretations of the mechanisms that constrain system transformation - explicitly and coherently addressing characteristics of reversibility and plausibility - and thus enabling integrative understanding of social-ecological system dynamics. Social media summary 'Lock-in' as a bridging concept for interdisciplinary understanding of barriers to desirable sustainability transitions.
32.	Dornelles, André Zuanazzi, et al. (författare) Transformation archetypes in global food systems 2022 Ingår i: Sustainability Science. - : Springer Science and Business Media LLC. - 1862-4065 .- 1862-4057. ; 17:5, s. 1827-1840 Tidskriftsartikel (refereegranskat)abstract Food systems are primary drivers of human and environmental health, but the understanding of their diverse and dynamic co-transformation remains limited. We use a data-driven approach to disentangle different development pathways of national food systems (i.e. ‘transformation archetypes’) based on historical, intertwined trends of food system structure (agricultural inputs and outputs and food trade), and social and environmental outcomes (malnutrition, biosphere integrity, and greenhouse gases emissions) for 161 countries, from 1995 to 2015. We found that whilst agricultural total factor productivity has consistently increased globally, a closer analysis suggests a typology of three transformation archetypes across countries: rapidly expansionist, expansionist, and consolidative. Expansionist and rapidly expansionist archetypes increased in agricultural area, synthetic fertilizer use, and gross agricultural output, which was accompanied by malnutrition, environmental pressures, and lasting socioeconomic disadvantages. The lowest rates of change in key structure metrics were found in the consolidative archetype. Across all transformation archetypes, agricultural greenhouse gases emissions, synthetic fertilizer use, and ecological footprint of consumption increased faster than the expansion of agricultural area, and obesity levels increased more rapidly than undernourishment decreased. The persistence of these unsustainable trajectories occurred independently of improvements in productivity. Our results underscore the importance of quantifying the multiple human and environmental dimensions of food systems transformations and can serve as a starting point to identify potential leverage points for sustainability transformations. More attention is thus warranted to alternative development pathways able of delivering equitable benefits to both productivity and to human and environmental health.
33.	Du Rietz, Ebba, et al. (författare) Mapping phenotypic and aetiological associations between ADHD and physical conditions in adulthood in Sweden : a genetically informed register study 2021 Ingår i: Lancet psychiatry. - : Elsevier. - 2215-0374 .- 2215-0366. ; 8:9, s. 774-783 Tidskriftsartikel (refereegranskat)abstract BACKGROUND: Emerging evidence suggests increased risk of several physical health conditions in people with ADHD. Only a few physical conditions have been thoroughly studied in relation to ADHD, and there is little knowledge on associations in older adults in particular. We aimed to investigate the phenotypic and aetiological associations between ADHD and a wide range of physical health conditions across adulthood.METHODS: We did a register study in Sweden and identified full-sibling and maternal half-sibling pairs born between Jan 1, 1932, and Dec 31, 1995, through the Population and Multi-Generation Registers. We excluded individuals who died or emigrated before Jan 1, 2005, and included full-siblings who were not twins and did not have half-siblings. ICD diagnoses were obtained from the National Patient Register. We extracted ICD diagnoses for physical conditions, when participants were aged 18 years or older, from inpatient (recorded 1973-2013) and outpatient (recorded 2001-13) services. Diagnoses were regarded as lifetime presence or absence. Logistic regression models were used to estimate the associations between ADHD (exposure) and 35 physical conditions (outcomes) in individuals and across sibling pairs. Quantitative genetic modelling was used to estimate the extent to which genetic and environmental factors accounted for the associations with ADHD.FINDINGS: 4 789 799 individuals were identified (2 449 146 [51%] men and 2 340 653 [49%] women), who formed 4 288 451 unique sibling pairs (3 819 207 full-sibling pairs and 469 244 maternal half-sibling pairs) and 1 841 303 family clusters (siblings, parents, cousins, spouses). The mean age at end of follow-up was 47 years (range 18-81; mean birth year 1966); ethnicity data were not available. Adults with ADHD had increased risk for most physical conditions (34 [97%] of 35) compared with adults without ADHD; the strongest associations were with nervous system disorders (eg, sleep disorders, epilepsy, dementia; odds ratios [ORs] 1·50-4·62) and respiratory diseases (eg, asthma, chronic obstructive pulmonary disease; ORs 2·42-3·24). Sex-stratified analyses showed similar patterns of results in men and women. Stronger cross-disorder associations were found between full-siblings than between half-siblings for nervous system, respiratory, musculoskeletal, and metabolic diseases (p<0·007). Quantitative genetic modelling showed that these associations were largely explained by shared genetic factors (60-69% of correlations), except for associations with nervous system disorders, which were mainly explained by non-shared environmental factors.INTERPRETATION: This mapping of aetiological sources of cross-disorder overlap can guide future research aiming to identify specific mechanisms contributing to risk of physical conditions in people with ADHD, which could ultimately inform preventive and lifestyle intervention efforts. Our findings highlight the importance of assessing the presence of physical conditions in patients with ADHD.FUNDING: Swedish Research Council; Swedish Brain Foundation; Swedish Research Council for Health, Working Life, and Welfare; Stockholm County Council; StratNeuro; EU Horizon 2020 research and innovation programme; National Institute of Mental Health.
34.	Döscher, Ralf, et al. (författare) The EC-Earth3 Earth system model for the Coupled Model Intercomparison Project 6 2022 Ingår i: Geoscientific Model Development. - : Copernicus GmbH. - 1991-959X .- 1991-9603. ; 15:7, s. 2973-3020 Tidskriftsartikel (refereegranskat)abstract The Earth system model EC-Earth3 for contributions to CMIP6 is documented here, with its flexible coupling framework, major model configurations, a methodology for ensuring the simulations are comparable across different high-performance computing (HPC) systems, and with the physical performance of base configurations over the historical period. The variety of possible configurations and sub-models reflects the broad interests in the EC-Earth community. EC-Earth3 key performance metrics demonstrate physical behavior and biases well within the frame known from recent CMIP models. With improved physical and dynamic features, new Earth system model (ESM) components, community tools, and largely improved physical performance compared to the CMIP5 version, EC-Earth3 represents a clear step forward for the only European community ESM. We demonstrate here that EC-Earth3 is suited for a range of tasks in CMIP6 and beyond.
35.	Giefing, Maciej, et al. (författare) Loss of function mutations of BCOR in classical Hodgkin lymphoma 2022 Ingår i: Leukemia and Lymphoma. - : Informa UK Limited. - 1042-8194 .- 1029-2403. ; 63:5, s. 1080-1090 Tidskriftsartikel (refereegranskat)abstract BCOR is a component of a variant Polycomb repressive complex 1 (PRC1.1). PRC1 and PRC2 complexes together constitute a major gene regulatory system critical for appropriate cellular differentiation. The gene is upregulated in germinal center (GC) B cells and mutated in a number of hematologic malignancies. We report BCOR inactivating alterations in 4/7 classic Hodgkin lymphoma (cHL) cell lines, subclonal somatic mutations in Hodgkin and Reed-Sternberg (HRS) cells of 4/10 cHL cases, and deletions in HRS cells of 7/17 primary cHL cases. In mice, conditional loss of Bcor driven by AID-Cre in GC B cells resulted in gene expression changes of 46 genes (>2-fold) including upregulated Lef1 that encodes a transcription factor responsible for establishing T-cell identity and Il9r (interleukin-9 receptor), an important member of the cytokine network in cHL. Our findings suggest a role for BCOR loss in cHL pathogenesis and GC-B cell homeostasis.
36.	Grinter, Rhys, et al. (författare) Structural basis for bacterial energy extraction from atmospheric hydrogen 2023 Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 615:7952, s. 541-547 Tidskriftsartikel (refereegranskat)abstract Diverse aerobic bacteria use atmospheric H2 as an energy source for growth and survival1. This globally significant process regulates the composition of the atmosphere, enhances soil biodiversity and drives primary production in extreme environments2,3. Atmospheric H2 oxidation is attributed to uncharacterized members of the [NiFe] hydrogenase superfamily4,5. However, it remains unresolved how these enzymes overcome the extraordinary catalytic challenge of oxidizing picomolar levels of H2 amid ambient levels of the catalytic poison O2 and how the derived electrons are transferred to the respiratory chain1. Here we determined the cryo-electron microscopy structure of the Mycobacterium smegmatis hydrogenase Huc and investigated its mechanism. Huc is a highly efficient oxygen-insensitive enzyme that couples oxidation of atmospheric H2 to the hydrogenation of the respiratory electron carrier menaquinone. Huc uses narrow hydrophobic gas channels to selectively bind atmospheric H2 at the expense of O2, and 3 [3Fe-4S] clusters modulate the properties of the enzyme so that atmospheric H2 oxidation is energetically feasible. The Huc catalytic subunits form an octameric 833 kDa complex around a membrane-associated stalk, which transports and reduces menaquinone 94 Å from the membrane. These findings provide a mechanistic basis for the biogeochemically and ecologically important process of atmospheric H2 oxidation, uncover a mode of energy coupling dependent on long-range quinone transport, and pave the way for the development of catalysts that oxidize H2 in ambient air.
37.	Hagendorff, Andreas, et al. (författare) Manual zur Indikation und Durchführung spezieller echokardiographischer Anwendungen 2021 Ingår i: Der Kardiologe. - : Springer Nature. - 1864-9718 .- 1864-9726. ; 15:6, s. 595-641 Tidskriftsartikel (refereegranskat)abstract The second manual on indications for and performance of echocardiography focusses on specific echocardiographic modalities and special problems in several patient cohorts. Practical aspects are discussed with priority. Established echocardiographic modalities are transesophageal, stress and contrast echocardiography. Modern technologies, such as 3D echocardiography and deformation imaging play an important role in nearly all scenarios of clinical echocardiography. This complete echocardiographic spectrum is incorporated into emergency and intensive care medicine, monitoring interventions of structural heart diseases, cardiac surgery, patients with cardiac assist devices, adult patients with congenital heart diseases and the care of highly infectious patients in pandemics. The diagnostic procedures of conventional and modern echocardiography are highlighted in this manual. The use of 3D echocardiography to characterize cardiac morphology and the application of deformation imaging to objectify cardiac function are already established in clinical practice. Stress echocardiography to detect myocardial ischemia and viability or to diagnose valvular heart diseases, assessment of coronary flow reserve to analyze myocardial perfusion and contrast echocardiography for left ventricular opacification and tumor characterization are increasingly being used to improve diagnostics. As mentioned for conventional echocardiography in the last manual of echocardiography in 2009, the modern features in echocardiography require standardized documentation and acquisition of certain images with optimized ultrasound settings, because conclusive and reproducible data analysis can only be performed if the image quality is sufficient.
38.	Hess, Timo, et al. (författare) Dissecting the genetic heterogeneity of gastric cancer 2023 Ingår i: EBioMedicine. - : Elsevier. - 2352-3964. ; 92 Tidskriftsartikel (refereegranskat)abstract Background: Gastric cancer (GC) is clinically heterogenous according to location (cardia/non-cardia) and histopathology (diffuse/intestinal). We aimed to characterize the genetic risk architecture of GC according to its subtypes. Another aim was to examine whether cardia GC and oesophageal adenocarcinoma (OAC) and its precursor lesion Barrett's oesophagus (BO), which are all located at the gastro-oesophageal junction (GOJ), share polygenic risk architecture.Methods: We did a meta-analysis of ten European genome-wide association studies (GWAS) of GC and its subtypes. All patients had a histopathologically confirmed diagnosis of gastric adenocarcinoma. For the identification of risk genes among GWAS loci we did a transcriptome-wide association study (TWAS) and expression quantitative trait locus (eQTL) study from gastric corpus and antrum mucosa. To test whether cardia GC and OAC/BO share genetic aetiology we also used a European GWAS sample with OAC/BO.Findings: Our GWAS consisting of 5816 patients and 10,999 controls highlights the genetic heterogeneity of GC according to its subtypes. We newly identified two and replicated five GC risk loci, all of them with subtype-specific association. The gastric transcriptome data consisting of 361 corpus and 342 antrum mucosa samples revealed that an upregulated expression of MUC1, ANKRD50, PTGER4, and PSCA are plausible GC-pathomechanisms at four GWAS loci. At another risk locus, we found that the blood-group 0 exerts protective effects for non-cardia and diffuse GC, while blood-group A increases risk for both GC subtypes. Furthermore, our GWAS on cardia GC and OAC/BO (10,279 patients, 16,527 controls) showed that both cancer entities share genetic aetiology at the polygenic level and identified two new risk loci on the single-marker level.Interpretation: Our findings show that the pathophysiology of GC is genetically heterogenous according to location and histopathology. Moreover, our findings point to common molecular mechanisms underlying cardia GC and OAC/BO.
39.	Hinkley, Sasha, et al. (författare) The JWST Early Release Science Program for the Direct Imaging and Spectroscopy of Exoplanetary Systems 2022 Ingår i: Publications of the Astronomical Society of the Pacific. - : IOP Publishing. - 0004-6280 .- 1538-3873. ; 134:1039 Tidskriftsartikel (refereegranskat)abstract The direct characterization of exoplanetary systems with high-contrast imaging is among the highest priorities for the broader exoplanet community. As large space missions will be necessary for detecting and characterizing exo-Earth twins, developing the techniques and technology for direct imaging of exoplanets is a driving focus for the community. For the first time, JWST will directly observe extrasolar planets at mid-infrared wavelengths beyond 5 μm, deliver detailed spectroscopy revealing much more precise chemical abundances and atmospheric conditions, and provide sensitivity to analogs of our solar system ice-giant planets at wide orbital separations, an entirely new class of exoplanet. However, in order to maximize the scientific output over the lifetime of the mission, an exquisite understanding of the instrumental performance of JWST is needed as early in the mission as possible. In this paper, we describe our 55 hr Early Release Science Program that will utilize all four JWST instruments to extend the characterization of planetary-mass companions to ∼15 μm as well as image a circumstellar disk in the mid-infrared with unprecedented sensitivity. Our program will also assess the performance of the observatory in the key modes expected to be commonly used for exoplanet direct imaging and spectroscopy, optimize data calibration and processing, and generate representative data sets that will enable a broad user base to effectively plan for general observing programs in future Cycles.
40.	Ho, Alan L., et al. (författare) Selumetinib Plus Adjuvant Radioactive Iodine in Patients with High-Risk Differentiated Thyroid Cancer : A Phase III, Randomized, Placebo-Controlled Trial (ASTRA) 2022 Ingår i: Journal of Clinical Oncology. - 0732-183X. ; 40:17, s. 1870-1878 Tidskriftsartikel (refereegranskat)abstract PURPOSESelumetinib can increase radioactive iodine (RAI) avidity in RAI-refractory tumors. We investigated whether selumetinib plus adjuvant RAI improves complete remission (CR) rates in patients with differentiated thyroid cancer (DTC) at high risk of primary treatment failure versus RAI alone.METHODSASTRA (ClinicalTrials.gov identifier: NCT01843062) is an international, phase III, randomized, placebo-controlled, double-blind trial. Patients with DTC at high risk of primary treatment failure (primary tumor > 4 cm; gross extrathyroidal extension outside the thyroid gland [T4 disease]; or N1a/N1b disease with ≥ 1 metastatic lymph node(s) ≥ 1 cm or ≥ 5 lymph nodes [any size]) were randomly assigned 2:1 to selumetinib 75 mg orally twice daily or placebo for approximately 5 weeks (no stratification). On treatment days 29-31, recombinant human thyroid-stimulating hormone (0.9 mg)-stimulated RAI (131I; 100 mCi/3.7 GBq) was administered, followed by 5 days of selumetinib/placebo. The primary end point (CR rate 18 months after RAI) was assessed in the intention-to-treat population.RESULTSFour hundred patients were enrolled (August 27, 2013-March 23, 2016) and 233 randomly assigned (selumetinib, n = 155 [67%]; placebo, n = 78 [33%]). No statistically significant difference in CR rate 18 months after RAI was observed (selumetinib n = 62 [40%]; placebo n = 30 [38%]; odds ratio 1.07 [95% CI, 0.61 to 1.87]; P =.8205). Treatment-related grade ≥ 3 adverse events were reported in 25/154 patients (16%) with selumetinib and none with placebo. The most common adverse event with selumetinib was dermatitis acneiform (n = 11 [7%]). No treatment-related deaths were reported.CONCLUSIONPostoperative pathologic risk stratification identified patients with DTC at high risk of primary treatment failure, although the addition of selumetinib to adjuvant RAI failed to improve the CR rate for these patients. Future strategies should focus on tumor genotype-tailored drug selection and maintaining drug dosing to optimize RAI efficacy.
41.	LeDuc, Richard D., et al. (författare) Proteomics Standards Initiative's ProForma 2.0 : Unifying the Encoding of Proteoforms and Peptidoforms br 2022 Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 21:4, s. 1189-1195 Tidskriftsartikel (refereegranskat)abstract It is important for the proteomics community to have a standardizedmanner to represent all possible variations of a protein or peptide primary sequence,including natural, chemically induced, and artifactual modifications. The HumanProteome Organization Proteomics Standards Initiative in collaboration with severalmembers of the Consortium for Top-Down Proteomics (CTDP) has developed astandard notation called ProForma 2.0, which is a substantial extension of the originalProForma notation developed by the CTDP. ProForma 2.0 aims to unify therepresentation of proteoforms and peptidoforms. ProForma 2.0 supports use casesneeded for bottom-up and middle-/top-down proteomics approaches and allows theencoding of highly modified proteins and peptides using a human- and machine-readable string. ProForma 2.0 can be used to represent protein modifications in a specified or ambiguous location, designated bymass shifts, chemical formulas, or controlled vocabulary terms, including cross-links (natural and chemical) and atomic isotopes.Notational conventions are based on public controlled vocabularies and ontologies. The most up-to-date full specification documentand information about software implementations are available athttp://psidev.info/proforma.
42.	Li, Lin, 1989-, et al. (författare) Attention-deficit/hyperactivity disorder symptoms and dietary habits in adulthood : A large population-based twin study in Sweden 2020 Ingår i: American Journal of Medical Genetics Part B. - : John Wiley & Sons. - 1552-4841 .- 1552-485X. ; 183:8, s. 475-485 Tidskriftsartikel (refereegranskat)abstract Associations between adult attention-deficit/hyperactivity disorder (ADHD) symptoms and dietary habits have not been well established and the underlying mechanisms remain unclear. We explored these associations using a Swedish population-based twin study with 17,999 individuals aged 20-47 years. We estimated correlations between inattention and hyperactivity/impulsivity with dietary habits and fitted twin models to determine the genetic and environmental contributions. Dietary habits were defined as (a) consumption of food groups, (b) consumption of food items rich in particular macronutrients, and (c) healthy and unhealthy dietary patterns. At the phenotypic level, inattention was positively correlated with seafood, high-fat, high-sugar, high-protein food consumptions, and unhealthy dietary pattern, with correlation coefficients ranging from 0.03 (95%CI: 0.01, 0.05) to 0.13 (95% CI: 0.11, 0.15). Inattention was negatively correlated with fruits, vegetables consumptions and healthy dietary pattern, with correlation coefficients ranging from -0.06 (95%CI: -0.08, -0.04) to -0.07 (95%CI: -0.09, -0.05). Hyperactivity/impulsivity and dietary habits showed similar but weaker patterns compared to inattention. All associations remained stable across age, sex and socioeconomic status. Nonshared environmental effects contributed substantially to the correlations of inattention (56-60%) and hyperactivity/impulsivity (63-80%) with dietary habits. The highest and lowest genetic correlations were between inattention and high-sugar food (rA = .16, 95% CI: 0.07, 0.25), and between hyperactivity/impulsivity and unhealthy dietary pattern (rA = .05, 95% CI: -0.05, 0.14), respectively. We found phenotypic and etiological overlap between ADHD and dietary habits, although these associations were weak. Our findings contribute to a better understanding of common etiological pathways between ADHD symptoms and various dietary habits.
43.	Lossow, Stefan, et al. (författare) A reassessment of the discrepancies in the annual variation of delta D-H2O in the tropical lower stratosphere between the MIPAS and ACE-FTS satellite data sets 2020 Ingår i: Atmospheric Measurement Techniques. - : Copernicus GmbH. - 1867-1381 .- 1867-8548. ; 13:1, s. 287-308 Tidskriftsartikel (refereegranskat)abstract The annual variation of delta D in the tropical lower stratosphere is a critical indicator for the relative importance of different processes contributing to the transport of water vapour through the cold tropical tropopause region into the stratosphere. Distinct observational discrepancies of the delta D annual variation were visible in the works of Steinwagner et al. (2010) and Randel et al. (2012). Steinwagner et al. (2010) analysed MIPAS (Michelson Interferometer for Passive Atmospheric Sounding) observations retrieved with the IMK/IAA (Institut fur Meteorologie und Klimaforschung in Karlsruhe, Germany, in collaboration with the Instituto de Astrofisica de Andalucia in Granada, Spain) processor, while Randel et al. (2012) focused on ACE-FTS (Atmospheric Chemistry Experiment Fourier Transform Spectrometer) observations. Here we reassess the discrepancies based on newer MIPAS (IMK/IAA) and ACE-FTS data sets, also showing for completeness results from SMR (Sub-Millimetre Radiometer) observations and a ECHAM/MESSy (European Centre for Medium-Range Weather Forecasts Hamburg and Modular Earth Sub-model System) Atmospheric Chemistry (EMAC) simulation (Eichinger et al., 2015b). Similar to the old analyses, the MIPAS data set yields a pronounced annual variation (maximum about 75 parts per thousand), while that derived from the ACE-FTS data set is rather weak (maximum about 25 parts per thousand). While all data sets exhibit the phase progression typical for the tape recorder, the annual maximum in the ACE-FTS data set precedes that in the MIPAS data set by 2 to 3 months. We critically consider several possible reasons for the observed discrepancies, focusing primarily on the MIPAS data set. We show that the delta D annual variation in the MIPAS data up to an altitude of 40 hPa is substantially impacted by a start altitude effect, i.e. dependency between the lowermost altitude where MIPAS retrievals are possible and retrieved data at higher altitudes. In itself this effect does not explain the differences with the ACE-FTS data. In addition, there is a mismatch in the vertical resolution of the MIPAS HDO and H2O data (being consistently better for HDO), which actually results in an artificial tape-recorder-like signal in delta D. Considering these MIPAS characteristics largely removes any discrepancies between the MIPAS and ACE-FTS data sets and shows that the MIPAS data are consistent with a delta D tape recorder signal with an amplitude of about 25 parts per thousand in the lowermost stratosphere.
44.	Luo, Xiyang, et al. (författare) A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics 2022 Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 21:6, s. 1566-1574 Tidskriftsartikel (refereegranskat)abstract Spectrum clustering is a powerful strategy to minimize redundant mass spectra by grouping them based on similarity, with the aim of forming groups of mass spectra from the same repeatedly measured analytes. Each such group of near-identical spectra can be represented by its so-called consensus spectrum for downstream processing. Although several algorithms for spectrum clustering have been adequately benchmarked and tested, the influence of the consensus spectrum generation step is rarely evaluated. Here, we present an implementation and benchmark of common consensus spectrum algorithms, including spectrum averaging, spectrum binning, the most similar spectrum, and the best-identified spectrum. We have analyzed diverse public data sets using two different clustering algorithms (spectra-duster and MaRaCluster) to evaluate how the consensus spectrum generation procedure influences downstream peptide identification. The BEST and BIN methods were found the most reliable methods for consensus spectrum generation, including for data sets with post-translational modifications (PTM) such as phosphorylation. All source code and data of the present study are freely available on GitHub at https://github.com/statisticalbiotechnology/representative-spectra-benchmark.
45.	Maire, Anne-Lise, et al. (författare) Design, pointing control, and on-sky performance of the mid-infrared vortex coronagraph for the VLT/NEAR experiment 2020 Ingår i: Journal of Astronomical Telescopes, Instruments, and Systems. - : SPIE-Intl Soc Optical Eng. - 2329-4221. ; 6:03, s. 1-16 Tidskriftsartikel (refereegranskat)
46.	Mak, Jonathan K L, et al. (författare) Genetic and environmental influences on longitudinal frailty trajectories from adulthood into old age. 2023 Ingår i: The journals of gerontology. Series A, Biological sciences and medical sciences. - : Oxford University Press (OUP). - 1758-535X. ; 78:2 Tidskriftsartikel (refereegranskat)abstract Frailty is a complex, dynamic geriatric condition, but limited evidence has shown how genes and environment may contribute to its longitudinal changes. We sought to investigate sources of individual differences in the longitudinal trajectories of frailty, considering potential selection bias when including a sample of oldest-old twins.Data were from two Swedish twin cohort studies: a younger cohort comprising 1,842 adults aged 29-96 years followed up to 15 waves, and an older cohort comprising 654 adults aged ≥79 years followed up to five waves. Frailty was measured using the frailty index (FI). Age-based latent growth curve models were used to examine longitudinal trajectories, and extended to a biometric analysis to decompose variability into genetic and environmental etiologies.A bilinear model with an inflection point at age 75 best described the data, indicating a four- to five-fold faster FI increase after 75 years. Twins from the older cohort had significantly higher mean FI at baseline but slower rate of increase afterwards. FI level at age 75 was moderately heritable in both men (42%) and women (55%). Genetic influences were relatively stable across age for men and increasing for women, although the most salient amplification in FI variability after age 75 was due to individual-specific environmental influences for both men and women; conclusions were largely consistent when excluding the older cohort.Increased heterogeneity of frailty in late life is mainly attributable to environmental influences, highlighting the importance of targeting environmental risk factors to mitigate frailty in older adults.
47.	O'Reilly, Lauren M., et al. (författare) The intergenerational transmission of suicidal behavior : an offspring of siblings study 2020 Ingår i: Translational Psychiatry. - : Nature Publishing Group. - 2158-3188. ; 10:1 Tidskriftsartikel (refereegranskat)abstract We examined the extent to which genetic factors shared across generations, measured covariates, and environmental factors associated with parental suicidal behavior (suicide attempt or suicide) account for the association between parental and offspring suicidal behavior. We used a Swedish cohort of 2,762,883 offspring born 1973-2001. We conducted two sets of analyses with offspring of half- and full-siblings: (1) quantitative behavior genetic models analyzing maternal suicidal behavior and (2) fixed-effects Cox proportional hazard models analyzing maternal and paternal suicidal behavior. The analyses also adjusted for numerous measured covariates (e.g., parental severe mental illness). Quantitative behavior genetic analyses found that 29.2% (95% confidence interval [CI], 5.29, 53.12%) of the intergenerational association was due to environmental factors associated with exposure to maternal suicidal behavior, with the remainder due to genetic factors. Statistical adjustment for parental behavioral health problems partially attenuated the environmental association; however, the results were no longer statistically significant. Cox hazard models similarly found that offspring were at a 2.74-fold increased risk [95% CI, 2.67, 2.83]) of suicidal behavior if their mothers attempted/died by suicide. After adjustment for familial factors and measured covariates, associations attenuated but remained elevated for offspring of discordant half-siblings (HR, 1.57 [95% CI, 1.45, 1.71]) and full-siblings (HR, 1.62 [95% CI, 1.57, 1.67]). Cox hazard models demonstrated a similar pattern between paternal and offspring suicidal behavior. This study found that the intergenerational transmission of suicidal behavior is largely due to shared genetic factors, as well as factors associated with parental behavioral health problems and environmental factors associated with parental suicidal behavior.
48.	Ostaszewski, Marek, et al. (författare) COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms 2021 Ingår i: Molecular Systems Biology. - : John Wiley & Sons. - 1744-4292 .- 1744-4292. ; 17:10 Tidskriftsartikel (refereegranskat)abstract We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.
49.	Reck, Kristian A., et al. (författare) Early-stage silver growth during sputter deposition on SiO2 and polystyrene - Comparison of biased DC magnetron sputtering, high-power impulse magnetron sputtering (HiPIMS) and bipolar HiPIMS 2024 Ingår i: Applied Surface Science. - : Elsevier BV. - 0169-4332 .- 1873-5584. ; 666 Tidskriftsartikel (refereegranskat)abstract The integration of silver thin films into optoelectronic devices has gained much interest due to their exceptional properties in terms of conductivity and compatibility with flexible substrates. For this type of application, ultrathin layers are desirable, because of their optical transparency. Standard direct current magnetron sputtering (DCMS) is known to lead to undesirable formation of islands at low effective film thicknesses on typical substrates like SiO2 or polystyrene (PS). Therefore, in this study, we explore high-power impulse magnetron sputtering (HiPIMS) with optional further acceleration of metal ions by biasing the substrate or an additional positive pulse (bipolar HiPIMS) for the fabrication of ultra-thin silver layers. The morphology and electrical properties of ultra-thin silver layers with selected effective thicknesses are characterized on SiO2 and PS substrates. The growth evolution of characteristic parameters is further investigated by in-situ grazing-incidence small-angle Xray scattering (GISAXS). The results show that HiPIMS deposition yields films with a higher density of clusters than DCMS leading to a percolation threshold at lower effective film thicknesses. This effect is amplified by further ion acceleration. Thus, we suggest HiPIMS as a promising technique for fabricating ultra-thin, conductive layers on organic and oxide substrates.
50.	Schinnerer, Eva, et al. (författare) PHANGS-JWST First Results : Rapid Evolution of Star Formation in the Central Molecular Gas Ring of NGC 1365 2023 Ingår i: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8205 .- 2041-8213. ; 944:2 Tidskriftsartikel (refereegranskat)abstract Large-scale bars can fuel galaxy centers with molecular gas, often leading to the development of dense ringlike structures where intense star formation occurs, forming a very different environment compared to galactic disks. We pair ∼0.″3 (30 pc) resolution new JWST/MIRI imaging with archival ALMA CO(2-1) mapping of the central ∼5 kpc of the nearby barred spiral galaxy NGC 1365 to investigate the physical mechanisms responsible for this extreme star formation. The molecular gas morphology is resolved into two well-known bright bar lanes that surround a smooth dynamically cold gas disk (R gal ∼ 475 pc) reminiscent of non-star-forming disks in early-type galaxies and likely fed by gas inflow triggered by stellar feedback in the lanes. The lanes host a large number of JWST-identified massive young star clusters. We find some evidence for temporal star formation evolution along the ring. The complex kinematics in the gas lanes reveal strong streaming motions and may be consistent with convergence of gas streamlines expected there. Indeed, the extreme line widths are found to be the result of inter-“cloud” motion between gas peaks; ScousePy decomposition reveals multiple components with line widths of 〈σ CO,scouse〉 ≈ 19 km s−1 and surface densities of 〈 Σ H 2 , scouse 〉 ≈ 800 M ⊙ pc − 2 , similar to the properties observed throughout the rest of the central molecular gas structure. Tailored hydrodynamical simulations exhibit many of the observed properties and imply that the observed structures are transient and highly time-variable. From our study of NGC 1365, we conclude that it is predominantly the high gas inflow triggered by the bar that is setting the star formation in its CMZ.

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