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Numrering	Referens	Omslagsbild	Hitta
1.	Kehoe, Laura, et al. (författare) Make EU trade with Brazil sustainable 2019 Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 364:6438, s. 341- Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
2.	Gross, Angelina S., et al. (författare) Acetyl-CoA carboxylase 1-dependent lipogenesis promotes autophagy downstream of AMPK 2019 Ingår i: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 294:32, s. 12020-12039 Tidskriftsartikel (refereegranskat)abstract Autophagy, a membrane-dependent catabolic process, ensures survival of aging cells and depends on the cellular energetic status. Acetyl-CoA carboxylase 1 (Acc1) connects central energy metabolism to lipid biosynthesis and is rate-limiting for the de novo synthesis of lipids. However, it is unclear how de novo lipogenesis and its metabolic consequences affect autophagic activity. Here, we show that in aging yeast, autophagy levels highly depend on the activity of Acc1. Constitutively active Acc1 (acc1(S/A)) or a deletion of the Acc1 negative regulator, Snf1 (yeast AMPK), shows elevated autophagy levels, which can be reversed by the Acc1 inhibitor soraphen A. Vice versa, pharmacological inhibition of Acc1 drastically reduces cell survival and results in the accumulation of Atg8-positive structures at the vacuolar membrane, suggesting late defects in the autophagic cascade. As expected, acc1(S/A) cells exhibit a reduction in acetate/acetyl-CoA availability along with elevated cellular lipid content. However, concomitant administration of acetate fails to fully revert the increase in autophagy exerted by acc1(S/A). Instead, administration of oleate, while mimicking constitutively active Acc1 in WT cells, alleviates the vacuolar fusion defects induced by Acc1 inhibition. Our results argue for a largely lipid-dependent process of autophagy regulation downstream of Acc1. We present a versatile genetic model to investigate the complex relationship between acetate metabolism, lipid homeostasis, and autophagy and propose Acc1-dependent lipogenesis as a fundamental metabolic path downstream of Snf1 to maintain autophagy and survival during cellular aging.
3.	Gross, Angelina S., et al. (författare) Acetyl-CoA carboxylase 1–dependent lipogenesis promotes autophagy downstream of AMPK 2019 Ingår i: Journal of Biological Chemistry. - : Elsevier. - 0021-9258 .- 1083-351X. ; 294:32, s. 12020-12039 Tidskriftsartikel (refereegranskat)abstract Autophagy, a membrane-dependent catabolic process, ensures survival of aging cells and depends on the cellular energetic status. Acetyl-CoA carboxylase 1 (Acc1) connects central energy metabolism to lipid biosynthesis and is rate-limiting for the de novo synthesis of lipids. However, it is unclear how de novo lipogenesis and its metabolic consequences affect autophagic activity. Here, we show that in aging yeast, autophagy levels highly depend on the activity of Acc1. Constitutively active Acc1 (acc1S/A) or a deletion of the Acc1 negative regulator, Snf1 (yeast AMPK), shows elevated autophagy levels, which can be reversed by the Acc1 inhibitor soraphen A. Vice versa, pharmacological inhibition of Acc1 drastically reduces cell survival and results in the accumulation of Atg8-positive structures at the vacuolar membrane, suggesting late defects in the autophagic cascade. As expected, acc1S/A cells exhibit a reduction in acetate/acetyl-CoA availability along with elevated cellular lipid content. However, concomitant administration of acetate fails to fully revert the increase in autophagy exerted by acc1S/A. Instead, administration of oleate, while mimicking constitutively active Acc1 in WT cells, alleviates the vacuolar fusion defects induced by Acc1 inhibition. Our results argue for a largely lipid-dependent process of autophagy regulation downstream of Acc1. We present a versatile genetic model to investigate the complex relationship between acetate metabolism, lipid homeostasis, and autophagy and propose Acc1-dependent lipogenesis as a fundamental metabolic path downstream of Snf1 to maintain autophagy and survival during cellular aging.
4.	Klionsky, Daniel J, et al. (författare) Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). 2016 Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 12:1, s. 1-222 Tidskriftsartikel (refereegranskat)
5.	Baum, R. P., et al. (författare) First-in-Humans Application of Tb-161: A Feasibility Study Using Tb-161-DOTATOC 2021 Ingår i: Journal of Nuclear Medicine. - : Society of Nuclear Medicine. - 0161-5505 .- 2159-662X. ; 62:10, s. 1391-1397 Tidskriftsartikel (refereegranskat)abstract Tb-161 has decay properties similar to those of Lu-177 but, additionally, emits a substantial number of conversion and Auger electrons. The aim of this study was to apply Tb-161 in a clinical setting and to investigate the feasibility of visualizing the physiologic and tumor biodistributions of Tb-161-DOTATOC. Methods: Tb-161 was shipped from Paul Scherrer Institute, Villigen-PSI, Switzerland, to Zentralklinik Bad Berka, Bad Berka, Germany, where it was used for the radiolabeling of DOTATOC. In 2 separate studies, 596 and 1,300 MBq of Tb-161-DOTATOC were administered to a 35-y-old male patient with a metastatic, well-differentiated, nonfunctional malignant paraganglioma and a 70-y-old male patient with a metastatic, functional neuroendocrine neoplasm of the pancreatic tail, respectively. Whole-body planar g-scintigraphy images were acquired over a period of several days for dosimetry calculations. SPECT/CT images were reconstructed using a recently established protocol and visually analyzed. Patients were observed for adverse events after the application of Tb-161-DOTATOC. Results: The radiolabeling of DOTATOC with Tb-161 was readily achieved with a high radiochemical purity suitable for patient application. Planar images and dosimetry provided the expected time-dependent biodistribution of Tb-161-DOTATOC in the liver, kidneys, spleen, and urinary bladder. SPECT/CT images were of high quality and visualized even small metastases in bones and liver. The application of Tb-161-DOTATOC was well tolerated, and no related adverse events were reported. Conclusion: This study demonstrated the feasibility of imaging even small metastases after the injection of relatively low activities of Tb-161-DOTATOC using g-scintigraphy and SPECT/CT. On the basis of this essential first step in translating Tb-161 to clinics, further efforts will be directed toward the application of Tb-161 for therapeutic purposes.
6.	Bergamaschi, Peter, et al. (författare) European Obspack compilation of atmospheric carbon dioxide data from ICOS and non-ICOS European stations for the period 1972-2023; : obspack_co2_466_GLOBALVIEWplus_v8.0_2023-04-26 2023 Annan publikation (övrigt vetenskapligt/konstnärligt)abstract This data package contains high accuracy CO2 dry air mole fractions from 58 ICOS and non-ICOS European observatories at in total 132 observation levels, collected by the ICOS Atmosphere Thematic Centre (ATC) and provided by the station contributors. The package is part of the Globalviewplus v8.0 data product, released in 2022 and is intended for use in carbon cycle inverse modeling, model evaluation, and satellite validation studies. Please report errors and send comments regarding this product to the ObsPack originators. Please read carefully the ObsPack Fair Use statement and cite appropriately. This is the sixth release of the GLOBALVIEWplus (GV+) cooperative data product. Please review the release notes for this product at www.esrl.noaa.gov/gmd/ccgg/obspack/release_notes.html. Metadata for this product are available at https://commons.datacite.org/doi.org/10.18160/CEC4-CAGK. Please visit http://www.gml.noaa.gov/ccgg/obspack/ for more information.
7.	Bruederle, Daniel, et al. (författare) A comprehensive workflow for general-purpose neural modeling with highly configurable neuromorphic hardware systems 2011 Ingår i: Biological Cybernetics. - : Springer Science and Business Media LLC. - 0340-1200 .- 1432-0770. ; 104:4-5, s. 263-296 Tidskriftsartikel (refereegranskat)abstract In this article, we present a methodological framework that meets novel requirements emerging from upcoming types of accelerated and highly configurable neuromorphic hardware systems. We describe in detail a device with 45 million programmable and dynamic synapses that is currently under development, and we sketch the conceptual challenges that arise from taking this platform into operation. More specifically, we aim at the establishment of this neuromorphic system as a flexible and neuroscientifically valuable modeling tool that can be used by non-hardware experts. We consider various functional aspects to be crucial for this purpose, and we introduce a consistent workflow with detailed descriptions of all involved modules that implement the suggested steps: The integration of the hardware interface into the simulator-independent model description language PyNN; a fully automated translation between the PyNN domain and appropriate hardware configurations; an executable specification of the future neuromorphic system that can be seamlessly integrated into this biology-to-hardware mapping process as a test bench for all software layers and possible hardware design modifications; an evaluation scheme that deploys models from a dedicated benchmark library, compares the results generated by virtual or prototype hardware devices with reference software simulations and analyzes the differences. The integration of these components into one hardware-software workflow provides an ecosystem for ongoing preparative studies that support the hardware design process and represents the basis for the maturity of the model-to-hardware mapping software. The functionality and flexibility of the latter is proven with a variety of experimental results.
8.	Liu, Jimmy Z, et al. (författare) Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis. 2013 Ingår i: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 45:6, s. 670-5 Tidskriftsartikel (refereegranskat)abstract Primary sclerosing cholangitis (PSC) is a severe liver disease of unknown etiology leading to fibrotic destruction of the bile ducts and ultimately to the need for liver transplantation. We compared 3,789 PSC cases of European ancestry to 25,079 population controls across 130,422 SNPs genotyped using the Immunochip. We identified 12 genome-wide significant associations outside the human leukocyte antigen (HLA) complex, 9 of which were new, increasing the number of known PSC risk loci to 16. Despite comorbidity with inflammatory bowel disease (IBD) in 72% of the cases, 6 of the 12 loci showed significantly stronger association with PSC than with IBD, suggesting overlapping yet distinct genetic architectures for these two diseases. We incorporated association statistics from 7 diseases clinically occurring with PSC in the analysis and found suggestive evidence for 33 additional pleiotropic PSC risk loci. Together with network analyses, these findings add to the genetic risk map of PSC and expand on the relationship between PSC and other immune-mediated diseases.
9.	Schewe, Jacob, et al. (författare) State-of-the-art global models underestimate impacts from climate extremes 2019 Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10 Tidskriftsartikel (refereegranskat)abstract Global impact models represent process-level understanding of how natural and human systems may be affected by climate change. Their projections are used in integrated assessments of climate change. Here we test, for the first time, systematically across many important systems, how well such impact models capture the impacts of extreme climate conditions. Using the 2003 European heat wave and drought as a historical analogue for comparable events in the future, we find that a majority of models underestimate the extremeness of impacts in important sectors such as agriculture, terrestrial ecosystems, and heat-related human mortality, while impacts on water resources and hydropower are overestimated in some river basins; and the spread across models is often large. This has important implications for economic assessments of climate change impacts that rely on these models. It also means that societal risks from future extreme events may be greater than previously thought.
10.	Wartenburger, Richard, et al. (författare) Evapotranspiration simulations in ISIMIP2a-Evaluation of spatio-temporal characteristics with a comprehensive ensemble of independent datasets 2018 Ingår i: Environmental Research Letters. - : IOP Publishing. - 1748-9326. ; 13:7 Tidskriftsartikel (refereegranskat)abstract Actual land evapotranspiration (ET) is a key component of the global hydrological cycle and an essential variable determining the evolution of hydrological extreme events under different climate change scenarios. However, recently available ET products show persistent uncertainties that are impeding a precise attribution of human-induced climate change. Here, we aim at comparing a range of independent global monthly land ET estimates with historical model simulations from the global water, agriculture, and biomes sectors participating in the second phase of the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP2a). Among the independent estimates, we use the EartH2Observe Tier-1 dataset (E2O), two commonly used reanalyses, a pre-compiled ensemble product (LandFlux-EVAL), and an updated collection of recently published datasets that algorithmically derive ET from observations or observations-based estimates (diagnostic datasets). A cluster analysis is applied in order to identify spatio-temporal differences among all datasets and to thus identify factors that dominate overall uncertainties. The clustering is controlled by several factors including the model choice, the meteorological forcing used to drive the assessed models, the data category (models participating in the different sectors of ISIMIP2a, E2O models, diagnostic estimates, reanalysis-based estimates or composite products), the ET scheme, and the number of soil layers in the models. By using these factors to explain spatial and spatio-temporal variabilities in ET, we find that the model choice mostly dominates (24%-40% of variance explained), except for spatio-temporal patterns of total ET, where the forcing explains the largest fraction of the variance (29%). The most dominant clusters of datasets are further compared with individual diagnostic and reanalysis-based estimates to assess their representation of selected heat waves and droughts in the Great Plains, Central Europe and western Russia. Although most of the ET estimates capture these extreme events, the generally large spread among the entire ensemble indicates substantial uncertainties.
11.	Abelev, Betty, et al. (författare) Long-range angular correlations on the near and away side in p-Pb collisions at root S-NN=5.02 TeV 2013 Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 719:1-3, s. 29-41 Tidskriftsartikel (refereegranskat)abstract Angular correlations between charged trigger and associated particles are measured by the ALICE detector in p-Pb collisions at a nucleon-nucleon centre-of-mass energy of 5.02 TeV for transverse momentum ranges within 0.5 < P-T,P-assoc < P-T,P-trig < 4 GeV/c. The correlations are measured over two units of pseudorapidity and full azimuthal angle in different intervals of event multiplicity, and expressed as associated yield per trigger particle. Two long-range ridge-like structures, one on the near side and one on the away side, are observed when the per-trigger yield obtained in low-multiplicity events is subtracted from the one in high-multiplicity events. The excess on the near-side is qualitatively similar to that recently reported by the CMS Collaboration, while the excess on the away-side is reported for the first time. The two-ridge structure projected onto azimuthal angle is quantified with the second and third Fourier coefficients as well as by near-side and away-side yields and widths. The yields on the near side and on the away side are equal within the uncertainties for all studied event multiplicity and p(T) bins, and the widths show no significant evolution with event multiplicity or p(T). These findings suggest that the near-side ridge is accompanied by an essentially identical away-side ridge. (c) 2013 CERN. Published by Elsevier B.V. All rights reserved.
12.	Abelev, Betty, et al. (författare) Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV 2012 Ingår i: Journal of High Energy Physics. - 1029-8479. ; :11 Tidskriftsartikel (refereegranskat)abstract The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at root s = 7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L-int = 5.6 nb(-1). The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p(t) > 1,3 GeV/c and rapidity vertical bar y vertical bar < 0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the psi(2S) and chi(c) resonances, is sigma(prompt J/psi) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 8.3 +/- 0.8(stat.) +/- 1.1 (syst.)(-1.4)(+1.5) (syst. pol.) mu b. The cross section for the production of b-hadrons decaying to J/psi with p(t) > 1.3 GeV/c and vertical bar y vertical bar < 0.9 is a sigma(J/psi <- hB) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 1.46 +/- 0.38 (stat.)(-0.32)(+0.26) (syst.) mu b. The results are compared to QCD model predictions. The shape of the p(t) and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b (b) over bar pair total cross section and d sigma/dy at mid-rapidity.
13.	Abelev, Betty, et al. (författare) Underlying Event measurements in pp collisions at root s=0.9 and 7 TeV with the ALICE experiment at the LHC 2012 Ingår i: Journal of High Energy Physics. - 1029-8479. ; :7 Tidskriftsartikel (refereegranskat)abstract We present measurements of Underlying Event observables in pp collisions at root s = 0 : 9 and 7 TeV. The analysis is performed as a function of the highest charged-particle transverse momentum p(T),L-T in the event. Different regions are defined with respect to the azimuthal direction of the leading (highest transverse momentum) track: Toward, Transverse and Away. The Toward and Away regions collect the fragmentation products of the hardest partonic interaction. The Transverse region is expected to be most sensitive to the Underlying Event activity. The study is performed with charged particles above three different p(T) thresholds: 0.15, 0.5 and 1.0 GeV/c. In the Transverse region we observe an increase in the multiplicity of a factor 2-3 between the lower and higher collision energies, depending on the track p(T) threshold considered. Data are compared to PYTHIA 6.4, PYTHIA 8.1 and PHOJET. On average, all models considered underestimate the multiplicity and summed p(T) in the Transverse region by about 10-30%.
14.	Abend, Sven, et al. (författare) Terrestrial very-long-baseline atom interferometry : Workshop summary 2024 Ingår i: AVS Quantum Science. - : American Institute of Physics (AIP). - 2639-0213. ; 6:2 Forskningsöversikt (refereegranskat)abstract This document presents a summary of the 2023 Terrestrial Very-Long-Baseline Atom Interferometry Workshop hosted by CERN. The workshop brought together experts from around the world to discuss the exciting developments in large-scale atom interferometer (AI) prototypes and their potential for detecting ultralight dark matter and gravitational waves. The primary objective of the workshop was to lay the groundwork for an international TVLBAI proto-collaboration. This collaboration aims to unite researchers from different institutions to strategize and secure funding for terrestrial large-scale AI projects. The ultimate goal is to create a roadmap detailing the design and technology choices for one or more kilometer--scale detectors, which will be operational in the mid-2030s. The key sections of this report present the physics case and technical challenges, together with a comprehensive overview of the discussions at the workshop together with the main conclusions.
15.	Bentham, James, et al. (författare) A century of trends in adult human height 2016 Ingår i: eLIFE. - : eLife Sciences Publications Ltd. - 2050-084X. ; 5 Tidskriftsartikel (refereegranskat)abstract Being taller is associated with enhanced longevity, and higher education and earnings. We reanalysed 1472 population-based studies, with measurement of height on more than 18.6 million participants to estimate mean height for people born between 1896 and 1996 in 200 countries. The largest gain in adult height over the past century has occurred in South Korean women and Iranian men, who became 20.2 cm (95% credible interval 17.5–22.7) and 16.5 cm (13.3– 19.7) taller, respectively. In contrast, there was little change in adult height in some sub-Saharan African countries and in South Asia over the century of analysis. The tallest people over these 100 years are men born in the Netherlands in the last quarter of 20th century, whose average heights surpassed 182.5 cm, and the shortest were women born in Guatemala in 1896 (140.3 cm; 135.8– 144.8). The height differential between the tallest and shortest populations was 19-20 cm a century ago, and has remained the same for women and increased for men a century later despite substantial changes in the ranking of countries.
16.	Bergamaschi, Peter, et al. (författare) High-resolution inverse modelling of European CH4emissions using the novel FLEXPART-COSMO TM5 4DVAR inverse modelling system 2022 Ingår i: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 22:20, s. 13243-13268 Tidskriftsartikel (refereegranskat)abstract We present a novel high-resolution inverse modelling system ("FLEXVAR") based on FLEXPARTCOSMO back trajectories driven by COSMO meteorological fields at 7 km×7 km resolution over the European COSMO-7 domain and the four-dimensional variational (4DVAR) data assimilation technique. FLEXVAR is coupled offline with the global inverse modelling system TM5-4DVAR to provide background mole fractions ("baselines") consistent with the global observations assimilated in TM5-4DVAR. We have applied the FLEXVAR system for the inverse modelling of European CH4 emissions in 2018 using 24 stations with in situ measurements, complemented with data from five stations with discrete air sampling (and additional stations outside the European COSMO-7 domain used for the global TM5-4DVAR inversions). The sensitivity of the FLEXVAR inversions to different approaches to calculate the baselines, different parameterizations of the model representation error, different settings of the prior error covariance parameters, different prior inventories, and different observation data sets are investigated in detail. Furthermore, the FLEXVAR inversions are compared to inversions with the FLEXPART extended Kalman filter ("FLExKF") system and with TM5-4DVAR inversions at 1° × 1° resolution over Europe. The three inverse modelling systems show overall good consistency of the major spatial patterns of the derived inversion increments and in general only relatively small differences in the derived annual total emissions of larger country regions. At the same time, the FLEXVAR inversions at 7 km × 7 km resolution allow the observations to be better reproduced than the TM5-4DVAR simulations at 1° × 1°. The three inverse models derive higher annual total CH4 emissions in 2018 for Germany, France, and BENELUX compared to the sum of anthropogenic emissions reported to UNFCCC and natural emissions estimated from the Global Carbon Project CH4 inventory, but the uncertainty ranges of top-down and bottom-up total emission estimates overlap for all three country regions. In contrast, the top-down estimates for the sum of emissions from the UK and Ireland agree relatively well with the total of anthropogenic and natural bottom-up inventories.
17.	Braungardt, Sibylle, et al. (författare) Renewable heating and cooling pathways – Towards full decarbonisation by 2050 – Final report 2023 Rapport (övrigt vetenskapligt/konstnärligt)abstract With the adoption of the EU Climate Law in 2021, the EU has set itself a binding target to achieve climate neutrality by 2050 and to reduce greenhouse gas emissions by 55 percent compared to 1990 levels by 2030. To support the increased ambition, the EU Commission adopted proposals for revising the key directives and regulations addressing energy efficiency, renewable energies and greenhouse gas emissions in the Fit for 55 package.The heating and cooling (H&C) sector plays a key role for reaching the EU energy and climate targets. H&C accounts for about 50 percent of the final energy consumption in the EU, and the sector is largely based on fossil fuels. In 2021, the share of renewable energies in H&C reached 23%. The decarbonisation of heating and cooling is addressed across several directives and regulations at EU level.The aim of this study is to support the analytical basis for the development and implementation of policies to ensure a seamless pathway to the full decarbonisation of the heating and cooling sector by 2050 in buildings and industry.
18.	Brett, Calvin, et al. (författare) Humidity-induced Nanoscale Restructuring in PEDOT:PSS and Cellulose reinforced Bio-based Organic Electronics Annan publikation (övrigt vetenskapligt/konstnärligt)
19.	Burgi, Matthias, et al. (författare) Processes and driving forces in changing cultural landscapes across Europe 2017 Ingår i: Landscape Ecology. - : Springer Science and Business Media LLC. - 0921-2973 .- 1572-9761. ; 32:11, s. 2097-2112 Tidskriftsartikel (refereegranskat)abstract ContextCultural landscapes evolve over time. However, the rate and direction of change might not be in line with societal needs and more information on the forces driving these changes are therefore needed.ObjectivesFilling the gap between single case studies and meta-analyses, we present a comparative study of landscape changes and their driving forces based in six regions across Europe conducted using a consistent method.MethodsA LULC analysis based on historical and contemporary maps from the nineteenth and twentieth century was combined with oral history interviews to learn more about perceived landscape changes, and remembered driving forces. Land cover and landscape changes were analysed regarding change, conversions and processes. For all case study areas, narratives on mapped land cover change, perceived landscape changes and driving forces were compiled.ResultsDespite a very high diversity in extent, direction and rates of change, a few dominant processes and widespread factors driving the changes could be identified in the six case study areas, i.e. access and infrastructure, political shifts, labor market, technological innovations, and for the more recent period climate change.ConclusionsGrasping peoples’ perception supplements the analyses of mapped land use and land cover changes and allows to address perceived landscape changes. The list of driving forces determined to be most relevant shows clear limits in predictability: Whereas changes triggered by infrastructural developments might be comparatively easy to model, political developments cannot be foreseen but might, nevertheless, leave major marks in the landscape.
20.	Burkhard, Benjamin, et al. (författare) Mapping and assessing ecosystem services in the EU - Lessons learned from the ESMERALDA approach of integration 2018 Ingår i: One Ecosystem. - : Pensoft Publishers. - 2367-8194. ; 3 Tidskriftsartikel (refereegranskat)abstract The European Union (EU) Horizon 2020 Coordination and Support Action ESMERALDA aimed at developing guidance and a flexible methodology for Mapping and Assessment of Ecosystems and their Services (MAES) to support the EU member states in the implementation of the EU Biodiversity Strategy’s Target 2 Action 5. ESMERALDA’s key tasks included network creation, stakeholder engagement, enhancing ecosystem services mapping and assessment methods across various spatial scales and value domains, work in case studies and support of EU member states in MAES implementation. Thus ESMERALDA aimed at integrating various project outcomes around four major strands: i) Networking, ii) Policy, iii) Research and iv) Application. The objective was to provide guidance for integrated ecosystem service mapping and assessment that can be used for sustainable decision-making in policy, business, society, practice and science at EU, national and regional levels. This article presents the overall ESMERALDA approach of integrating the above-mentioned project components and outcomes and provides an overview of how the enhanced methods were applied and how they can be used to support MAES implementation in the EU member states. Experiences with implementing such a large pan-European Coordination and Support Action in the context of EU policy are discussed and recommendations for future actions are given.
21.	Chen, Z, et al. (författare) Importance of heterotrophic nitrification and dissimilatory nitrate reduction to ammonium in a cropland soil: Evidences from a 15N tracing study to literature synthesis 2015 Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 91, s. 65-75 Tidskriftsartikel (refereegranskat)abstract Future climate change is predicted to influence soil moisture regime, a key factor regulating soil nitrogen (N) cycling. To elucidate how soil moisture affects gross N transformation in a cultivated black soil, a 15N tracing study was conducted at 30%, 50% and 70% water-filled pore space (WFPS). While gross mineralization rate of recalcitrant organic N (Nrec) increased from 0.56 to 2.47 mg N kg−1 d−1, the rate of labile organic N mineralization declined from 4.23 to 2.41 mg N kg−1 d−1 with a WFPS increase from 30% to 70%. Similar to total mineralization, no distinct moisture effect was found on total immobilization of ammonium, which primarily entered the Nrec pool. Nitrate (NO3−) was mainly produced via autotrophic nitrification, which was significantly stimulated by increasing WFPS. Unexpectedly, heterotrophic nitrification was observed, with the highest rate of 1.06 mg N kg−1 d−1 at 30% WFPS, contributing 31.8% to total NO3− production, and decreased with WFPS. Dissimilatory nitrate reduction to ammonium (DNRA) increased from near zero (30% WFPS) to 0.26 mg N kg−1 d−1 (70% WFPS), amounting to 16.7–92.9% of NO3− consumption. A literature synthetic analysis from global multiple ecosystems showed that the rates of heterotrophic nitrification and DNRA in test soil were comparative to the forest and grassland ecosystems, and that heterotrophic nitrification was positively correlated with precipitation, soil organic carbon (SOC) and C/N, but negatively with pH and bulk density, while DNRA showed positive relationships with precipitation, clay, SOC, C/NO3− and WFPS. We suggested that low pH and bulk density and high SOC and C/N in test soil might favor heterotrophic nitrification, and that C and NO3− availability together with anaerobic condition were crucial for DNRA. Overall, our study highlights the role of moisture in regulating gross N turnover and the importance of heterotrophic nitrification for NO3− production under low moisture and DNRA for NO3− retention under high moisture in cropland.
22.	Christakoudi, Sofia, et al. (författare) A Body Shape Index (ABSI) achieves better mortality risk stratification than alternative indices of abdominal obesity : results from a large European cohort 2020 Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 10:1 Tidskriftsartikel (refereegranskat)abstract Abdominal and general adiposity are independently associated with mortality, but there is no consensus on how best to assess abdominal adiposity. We compared the ability of alternative waist indices to complement body mass index (BMI) when assessing all-cause mortality. We used data from 352,985 participants in the European Prospective Investigation into Cancer and Nutrition (EPIC) and Cox proportional hazards models adjusted for other risk factors. During a mean follow-up of 16.1 years, 38,178 participants died. Combining in one model BMI and a strongly correlated waist index altered the association patterns with mortality, to a predominantly negative association for BMI and a stronger positive association for the waist index, while combining BMI with the uncorrelated A Body Shape Index (ABSI) preserved the association patterns. Sex-specific cohort-wide quartiles of waist indices correlated with BMI could not separate high-risk from low-risk individuals within underweight (BMI<18.5 kg/m(2)) or obese (BMI30 kg/m(2)) categories, while the highest quartile of ABSI separated 18-39% of the individuals within each BMI category, which had 22-55% higher risk of death. In conclusion, only a waist index independent of BMI by design, such as ABSI, complements BMI and enables efficient risk stratification, which could facilitate personalisation of screening, treatment and monitoring.
23.	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.
24.	de Jong, Yde, et al. (författare) PESI - a taxonomic backbone for Europe 2015 Ingår i: Biodiversity Data Journal. - 1314-2836 .- 1314-2828. ; 3, s. 1-51 Tidskriftsartikel (refereegranskat)abstract Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools.The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information.This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs.
25.	Di Cesare, Mariachiara, et al. (författare) Trends in adult body-mass index in 200 countries from 1975 to 2014: A pooled analysis of 1698 population-based measurement studies with 19.2 million participants 2016 Ingår i: The Lancet. - : Lancet Publishing Group. - 0140-6736 .- 1474-547X. ; 387:10026, s. 1377-1396 Tidskriftsartikel (refereegranskat)
26.	Dvirnas, Albertas, et al. (författare) Detection of structural variations in densely-labelled optical DNA barcodes: A hidden Markov model approach 2021 Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 16:11 Tidskriftsartikel (refereegranskat)abstract Large-scale genomic alterations play an important role in disease, gene expression, and chromosome evolution. Optical DNA mapping (ODM), commonly categorized into sparsely-labelled ODM and densely-labelled ODM, provides sequence-specific continuous intensity profiles (DNA barcodes) along single DNA molecules and is a technique well-suited for detecting such alterations. For sparsely-labelled barcodes, the possibility to detect large genomic alterations has been investigated extensively, while densely-labelled barcodes have not received as much attention. In this work, we introduce HMMSV, a hidden Markov model (HMM) based algorithm for detecting structural variations (SVs) directly in densely-labelled barcodes without access to sequence information. We evaluate our approach using simulated data-sets with 5 different types of SVs, and combinations thereof, and demonstrate that the method reaches a true positive rate greater than 80% for randomly generated barcodes with single variations of size 25 kilobases (kb). Increasing the length of the SV further leads to larger true positive rates. For a real data-set with experimental barcodes on bacterial plasmids, we successfully detect matching barcode pairs and SVs without any particular assumption of the types of SVs present. Instead, our method effectively goes through all possible combinations of SVs. Since ODM works on length scales typically not reachable with other techniques, our methodology is a promising tool for identifying arbitrary combinations of genomic alterations.
27.	Dvirnas, Albertas, et al. (författare) Facilitated sequence assembly using densely labeled optical DNA barcodes: A combinatorial auction approach 2018 Ingår i: Plos One. - : Public Library of Science (PLoS). - 1932-6203. ; 13:3 Tidskriftsartikel (refereegranskat)abstract The output from whole genome sequencing is a set of contigs, i.e. short non-overlapping DNA sequences (sizes 1-100 kilobasepairs). Piecing the contigs together is an especially difficult task for previously unsequenced DNA, and may not be feasible due to factors such as the lack of sufficient coverage or larger repetitive regions which generate gaps in the final sequence. Here we propose a new method for scaffolding such contigs. The proposed method uses densely labeled optical DNA barcodes from competitive binding experiments as scaffolds. On these scaffolds we position theoretical barcodes which are calculated from the contig sequences. This allows us to construct longer DNA sequences from the contig sequences. This proof-of-principle study extends previous studies which use sparsely labeled DNA barcodes for scaffolding purposes. Our method applies a probabilistic approach that allows us to discard "foreign" contigs from mixed samples with contigs from different types of DNA. We satisfy the contig non-overlap constraint by formulating the contig placement challenge as a combinatorial auction problem. Our exact algorithm for solving this problem reduces computational costs compared to previous methods in the combinatorial auction field. We demonstrate the usefulness of the proposed scaffolding method both for synthetic contigs and for contigs obtained using Illumina sequencing for a mixed sample with plasmid and chromosomal DNA.
28.	Ericson, Åsa, et al. (författare) Product-service systems : from customer needs to requirements in early development phases 2009 Ingår i: Industrial product-service systems (IPS2). - Cranfield : Cranfield University Press. - 9780955743658 Konferensbidrag (refereegranskat)
29.	Ericsson, Åsa, et al. (författare) Product-service systems - From customer needs to requirements in early development phases 2009 Konferensbidrag (refereegranskat)abstract Framed by Product-Service Systems (PSS), this paper discuss how needs and requirements are applied in early phases. In product development literature these and closely related terms are mixed, and a focus on gathering customer information about goods and their use guides the development team. This theoretical study highlights that lifecycle commitments such as PSS insist on the generation of a broader information basis. The application of a divergent view on goods, their use and the customers is likely to provide such information basis. The discussion provides a proposal of a simple model to set needs and requirements in relation.
30.	Franke, James A, et al. (författare) Agricultural breadbaskets shift poleward given adaptive farmer behavior under climate change 2022 Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 28:1, s. 167-181 Tidskriftsartikel (refereegranskat)abstract Modern food production is spatially concentrated in global "breadbaskets". A major unresolved question is whether these peak production regions will shift poleward as the climate warms, allowing some recovery of potential climaterelated losses. While agricultural impacts studies to date have focused on currently cultivated land, the Global Gridded Crop Model Intercomparison Project (GGCMI) Phase 2 experiment allows us to assess changes in both yields and the location of peak productivity regions under warming. We examine crop responses under projected end-of-century warming using 7 process-based models simulating 5 major crops (maize, rice, soybeans, and spring and winter wheat) with a variety of adaptation strategies. We find that in no-adaptation cases, when planting date and cultivar choices are held fixed, regions of peak production remain stationary and yield losses can be severe, since growing seasons contract strongly with warming. When adaptations in management practices are allowed (cultivars that retain growing season length under warming and modified planting dates), peak productivity zones shift poleward and yield losses are largely recovered. While most growing-zone shifts are ultimately limited by geography, breadbaskets studied here move poleward over 600 km on average by end of the century under RCP8.5. These results suggest that agricultural impacts assessments can be strongly biased if restricted in spatial area or in the scope of adaptive behavior considered. Accurate evaluation of food security under climate change requires global modeling and careful treatment of adaptation strategies.
31.	Franke, James A., et al. (författare) The GGCMI Phase 2 emulators : Global gridded crop model responses to changes in CO2, temperature, water, and nitrogen (version 1.0) 2020 Ingår i: Geoscientific Model Development. - : Copernicus GmbH. - 1991-959X .- 1991-9603. ; 13:9, s. 3995-4018 Tidskriftsartikel (refereegranskat)abstract Statistical emulation allows combining advantageous features of statistical and process-based crop models for understanding the effects of future climate changes on crop yields. We describe here the development of emulators for nine process-based crop models and five crops using output from the Global Gridded Model Intercomparison Project (GGCMI) Phase 2. The GGCMI Phase 2 experiment is designed with the explicit goal of producing a structured training dataset for emulator development that samples across four dimensions relevant to crop yields: Atmospheric carbon dioxide (CO2) concentrations, temperature, water supply, and nitrogen inputs (CTWN). Simulations are run under two different adaptation assumptions: That growing seasons shorten in warmer climates, and that cultivar choice allows growing seasons to remain fixed. The dataset allows emulating the climatological-mean yield response of all models with a simple polynomial in mean growing-season values. Climatological-mean yields are a central metric in climate change impact analysis; we show here that they can be captured without relying on interannual variations. In general, emulation errors are negligible relative to differences across crop models or even across climate model scenarios; errors become significant only in some marginal lands where crops are not currently grown. We demonstrate that the resulting GGCMI emulators can reproduce yields under realistic future climate simulations, even though the GGCMI Phase 2 dataset is constructed with uniform CTWN offsets, suggesting that the effects of changes in temperature and precipitation distributions are small relative to those of changing means. The resulting emulators therefore capture relevant crop model responses in a lightweight, computationally tractable form, providing a tool that can facilitate model comparison, diagnosis of interacting factors affecting yields, and integrated assessment of climate impacts.
32.	Franke, James A., et al. (författare) The GGCMI Phase 2 experiment : Global gridded crop model simulations under uniform changes in CO2, temperature, water, and nitrogen levels (protocol version 1.0) 2020 Ingår i: Geoscientific Model Development. - : Copernicus GmbH. - 1991-959X .- 1991-9603. ; 13:5, s. 2315-2336 Tidskriftsartikel (refereegranskat)abstract Concerns about food security under climate change motivate efforts to better understand future changes in crop yields. Process-based crop models, which represent plant physiological and soil processes, are necessary tools for this purpose since they allow representing future climate and management conditions not sampled in the historical record and new locations to which cultivation may shift. However, process-based crop models differ in many critical details, and their responses to different interacting factors remain only poorly understood. The Global Gridded Crop Model Intercomparison (GGCMI) Phase 2 experiment, an activity of the Agricultural Model Intercomparison and Improvement Project (AgMIP), is designed to provide a systematic parameter sweep focused on climate change factors and their interaction with overall soil fertility, to allow both evaluating model behavior and emulating model responses in impact assessment tools. In this paper we describe the GGCMI Phase 2 experimental protocol and its simulation data archive. A total of 12 crop models simulate five crops with systematic uniform perturbations of historical climate, varying CO2, temperature, water supply, and applied nitrogen ("CTWN") for rainfed and irrigated agriculture, and a second set of simulations represents a type of adaptation by allowing the adjustment of growing season length. We present some crop yield results to illustrate general characteristics of the simulations and potential uses of the GGCMI Phase 2 archive. For example, in cases without adaptation, modeled yields show robust decreases to warmer temperatures in almost all regions, with a nonlinear dependence that means yields in warmer baseline locations have greater temperature sensitivity. Inter-model uncertainty is qualitatively similar across all the four input dimensions but is largest in high-latitude regions where crops may be grown in the future.
33.	Gaine, Sean, et al. (författare) Risk status at selexipag initiation in pulmonary arterial hypertension (PAH) : Insights from EXPOSURE 2020 Ingår i: European Respiratory Journal. - : European Respiratory Society. - 0903-1936 .- 1399-3003. ; 56 Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
34.	Gaine, Sean, et al. (författare) Selexipag in patients with pulmonary arterial hypertension associated with connective tissue disease (PAH-CTD) : real-world experience from EXPOSURE 2024 Ingår i: Pulmonary Circulation. - : John Wiley & Sons. - 2045-8932 .- 2045-8940. ; 14:3 Tidskriftsartikel (refereegranskat)abstract Selexipag is indicated for the treatment of pulmonary arterial hypertension (PAH), including PAH associated with connective tissue disease (CTD), and further insights into the management of selexipag-treated PAH-CTD patients in clinical settings are needed. These analyses of the ongoing, multicenter, prospective EXPOSURE (EUPAS19085) study describe characteristics, treatment patterns, tolerability, and outcomes of PAH-CTD patients initiating selexipag in Europe/Canada. All analyses were descriptive, with idiopathic PAH patients who typically display better prognosis included for context. Six hundred ninety-eight selexipag-treated patients had follow-up information; 178 (26%) had PAH-CTD. The median age was 68 years, patients were predominantly female (88%), and with WHO functional class III symptoms (63%); the median time since diagnosis was 1.7 years. There were 5% patients at low, 25% intermediate-low, 40% intermediate-high, and 30% high risk of 1-year mortality, according to the ESC/ERS 4-strata risk score. Most (80%) initiated selexipag as a triple oral therapy, and most of these (62%) remained on triple therapy 6 months post-baseline. Over a median (Q1−Q3) selexipag exposure period of 8.6 (2.5−17.2) months, 79 (44%) patients discontinued selexipag; 36 (20%) due to tolerability/adverse events. Sixty (34%) patients were hospitalized at least once; 120 hospitalizations occurred, with 49 (48%) deemed PAH-related. Survival at 1 year was 85%, and at 2 years was 71%; 29 (16%) patients died. These results describe the use of combination therapy with selexipag for patients with PAH-CTD. These findings suggest an opportunity to optimize the benefits of selexipag among patients with PAH-CTD by moving from escalating after years in response to clinical deterioration to escalating sooner to prevent clinical deterioration.
35.	Gao, Yu, et al. (författare) Immunodeficiency syndromes differentially impact the functional profile of SARS-CoV-2-specific T cells elicited by mRNA vaccination 2022 Ingår i: Immunity. - : Elsevier. - 1074-7613 .- 1097-4180. ; 55:9, s. 1732-1746.e5 Tidskriftsartikel (refereegranskat)abstract Many immunocompromised patients mount suboptimal humoral immunity after SARS-CoV-2 mRNA vaccination. Here, we assessed the single-cell profile of SARS-CoV-2-specific T cells post-mRNA vaccination in healthy individuals and patients with various forms of immunodeficiencies. Impaired vaccine-induced cell-mediated immunity was observed in many immunocompromised patients, particularly in solid-organ transplant and chronic lymphocytic leukemia patients. Notably, individuals with an inherited lack of mature B cells, i.e., X-linked agammaglobulinemia (XLA) displayed highly functional spike-specific T cell responses. Single-cell RNA-sequencing further revealed that mRNA vaccination induced a broad functional spectrum of spike-specific CD4+ and CD8+ T cells in healthy individuals and patients with XLA. These responses were founded on polyclonal repertoires of CD4+ T cells and robust expansions of oligoclonal effector-memory CD45RA+ CD8+ T cells with stem-like characteristics. Collectively, our data provide the functional continuum of SARS-CoV-2-specific T cell responses post-mRNA vaccination, highlighting that cell-mediated immunity is of variable functional quality across immunodeficiency syndromes.
36.	Gergei, Ingrid, et al. (författare) GWAS META-analysis followed by MENDELIAN randomisation revealed potential control mechanisms for circulating α-klotho levels. 2022 Ingår i: Human molecular genetics. - : Oxford University Press (OUP). - 1460-2083 .- 0964-6906. ; 31:5, s. 792-802 Tidskriftsartikel (refereegranskat)abstract The protein α-Klotho acts as transmembrane the co-receptor for fibroblast growth factor 23 (FGF-23) and is a key regulator of phosphate homeostasis. However, α-Klotho also exists in a circulating form, with pleiotropic, but incompletely understood functions and regulation. Therefore, we undertook a GWAS meta-analysis followed by Mendelian randomisation (MR) of circulating α-Klotho levels.Plasma α-Klotho levels were measured by ELISA in the LURIC and ALSPAC (mothers) cohorts, followed by a GWAS meta-analysis in 4376 individuals across the two cohorts.Six signals at five loci were associated with circulating α-Klotho levels at genome-wide significance (p<5×10-8), namely ABO, KL, FGFR1, and two post-translational modification genes, B4GALNT3 and CHST9. Together, these loci explained >9% of the variation in circulating α-Klotho levels. MR analyses revealed no causal relationships between α-Klotho and renal function, FGF-23-dependent factors such as vitamin D and phosphate levels, or bone mineral density. The screening for genetic correlations with other phenotypes, followed by targeted MR suggested causal effects of liability of Crohn's disease risk [IVW beta=0.059 (95% CI 0.026, 0.093)] and low-density lipoprotein cholesterol (LDL-C) levels [-0.198, (-0.332, -0.063)] on α-Klotho.Our GWAS findings suggest that two enzymes involved in post-translational modification, B4GALNT3 and CHST9, contribute to genetic influences on α-Klotho levels, presumably by affecting protein turnover and stability. Subsequent evidence from MR analyses on α-Klotho levels suggest regulation by mechanisms besides phosphate-homeostasis and raise the possibility of cross-talk with FGF19- and FGF21-dependent pathways, respectively.
37.	Gordon, I.E., et al. (författare) The HITRAN2020 molecular spectroscopic database 2022 Ingår i: Journal of Quantitative Spectroscopy and Radiative Transfer. - : Elsevier. - 0022-4073 .- 1879-1352. ; 277 Tidskriftsartikel (refereegranskat)abstract The HITRAN database is a compilation of molecular spectroscopic parameters. It was established in the early 1970s and is used by various computer codes to predict and simulate the transmission and emission of light in gaseous media (with an emphasis on terrestrial and planetary atmospheres). The HITRAN compilation is composed of five major components: the line-by-line spectroscopic parameters required for high-resolution radiative-transfer codes, experimental infrared absorption cross-sections (for molecules where it is not yet feasible for representation in a line-by-line form), collision-induced absorption data, aerosol indices of refraction, and general tables (including partition sums) that apply globally to the data. This paper describes the contents of the 2020 quadrennial edition of HITRAN. The HITRAN2020 edition takes advantage of recent experimental and theoretical data that were meticulously validated, in particular, against laboratory and atmospheric spectra. The new edition replaces the previous HITRAN edition of 2016 (including its updates during the intervening years). All five components of HITRAN have undergone major updates. In particular, the extent of the updates in the HITRAN2020 edition range from updating a few lines of specific molecules to complete replacements of the lists, and also the introduction of additional isotopologues and new (to HITRAN) molecules: SO, CH3F, GeH4, CS2, CH3I and NF3. Many new vibrational bands were added, extending the spectral coverage and completeness of the line lists. Also, the accuracy of the parameters for major atmospheric absorbers has been increased substantially, often featuring sub-percent uncertainties. Broadening parameters associated with the ambient pressure of water vapor were introduced to HITRAN for the first time and are now available for several molecules. The HITRAN2020 edition continues to take advantage of the relational structure and efficient interface available at www.hitran.org and the HITRAN Application Programming Interface (HAPI). The functionality of both tools has been extended for the new edition.
38.	Hadad, Ronza, 1984-, et al. (författare) A Chlamydia trachomatis 23S rRNA G1523A variant escaping detection in the Aptima Combo 2 assay (Hologic) was widespread across Denmark in July-September 2019 2020 Ingår i: Acta Pathologica, Microbiologica et Immunologica Scandinavica (APMIS). - : Wiley-Blackwell Publishing Inc.. - 0903-4641 .- 1600-0463. ; 128:6, s. 440-444 Tidskriftsartikel (refereegranskat)abstract Chlamydia trachomatis infection is the most common bacterial sexually transmitted infection globally, and nucleic acid amplification tests (NAATs) are recommended for highly sensitive and specific diagnosis. In early 2019, the Finnish new variant of Chlamydia trachomatis (FI-nvCT) was identified. The FI-nvCT has a C1515T mutation in the 23S rRNA gene, making it escaping detection in the Aptima Combo 2 (AC2; Hologic) NAAT, and the FI-nvCT has been subsequently reported in Sweden and Norway. In the present study, we investigated the presence of the FI-nvCT and other AC2 diagnostic-escape CT mutants in July-September 2019 in Denmark. The FI-nvCT was present but rare in Denmark. However, another AC2 diagnostic-escape CT mutant (with a 23S rRNA G1523A mutation) was found to be widespread across Denmark, accounting for 95% (76/80) of AC2 diagnostic-escape nvCT samples from five Danish CT-diagnostic laboratories. This nvCT-G1523A has previously only been detected in one single sample in the United Kingdom and Norway, respectively. It is vital to monitor the continued stability of the NAAT targets in local, national and international settings and monitor as well as appropriately analyse incidence, unexplained shifts in diagnostics rates, and/or annual collections of samples diagnosed as negative/equivocal using NAATs with different target(s). Furthermore, diagnostic CT NAATs with dual target sequences are crucial and fortunately, an updated Hologic AC2 assay including one additional target sequence is in advanced development.
39.	Huygens, Dries, et al. (författare) Biogeochemical Nitrogen Cycling in Wetland Ecosystem: Nitrogen-15 Isotope Techniques 2013 Ingår i: Methods in Biogeochemistry of Wetlands. R.D. DeLaune, K.R. Reddy, C.J. Richardson, and J.P. Megonigal (eds.). - Madison, WI, USA : Soil Science Society of America, Inc.. - 9780891189602 ; , s. 553-592 Bokkapitel (refereegranskat)
40.	Iarko, V., et al. (författare) Extension of nanoconfined DNA: Quantitative comparison between experiment and theory 2015 Ingår i: Physical Review E (Statistical, Nonlinear, and Soft Matter Physics). - 1539-3755 .- 1550-2376. ; 92:6, s. Art. Nr. 062701- Tidskriftsartikel (refereegranskat)abstract The extension of DNA confined to nanochannels has been studied intensively and in detail. However, quantitative comparisons between experiments and model calculations are difficult because most theoretical predictions involve undetermined prefactors, and because the model parameters (contour length, Kuhn length, effective width) are difficult to compute reliably, leading to substantial uncertainties. Here we use a recent asymptotically exact theory for the DNA extension in the "extended de Gennes regime" that allows us to compare experimental results with theory. For this purpose, we performed experiments measuring the mean DNA extension and its standard deviation while varying the channel geometry, dye intercalation ratio, and ionic strength of the buffer. The experimental results agree very well with theory at high ionic strengths, indicating that the model parameters are reliable. At low ionic strengths, the agreement is less good. We discuss possible reasons. In principle, our approach allows us to measure the Kuhn length and the effective width of a single DNA molecule and more generally of semiflexible polymers in solution.
41.	Jimenez-del-Toro, Oscar, et al. (författare) Cloud-Based Evaluation of Anatomical Structure Segmentation and Landmark Detection Algorithms : VISCERAL Anatomy Benchmarks 2016 Ingår i: IEEE Transactions on Medical Imaging. - : Institute of Electrical and Electronics Engineers (IEEE). - 0278-0062 .- 1558-254X. ; 35:11, s. 2459-2475 Tidskriftsartikel (refereegranskat)abstract Variations in the shape and appearance of anatomical structures in medical images are often relevant radiological signs of disease. Automatic tools can help automate parts of this manual process. A cloud-based evaluation framework is presented in this paper including results of benchmarking current state-of-the-art medical imaging algorithms for anatomical structure segmentation and landmark detection: the VISCERAL Anatomy benchmarks. The algorithms are implemented in virtual machines in the cloud where participants can only access the training data and can be run privately by the benchmark administrators to objectively compare their performance in an unseen common test set. Overall, 120 computed tomography and magnetic resonance patient volumes were manually annotated to create a standard Gold Corpus containing a total of 1295 structures and 1760 landmarks. Ten participants contributed with automatic algorithms for the organ segmentation task, and three for the landmark localization task. Different algorithms obtained the best scores in the four available imaging modalities and for subsets of anatomical structures. The annotation framework, resulting data set, evaluation setup, results and performance analysis from the three VISCERAL Anatomy benchmarks are presented in this article. Both the VISCERAL data set and Silver Corpus generated with the fusion of the participant algorithms on a larger set of non-manually-annotated medical images are available to the research community.
42.	Johnning, Anna, 1985, et al. (författare) The resistomes of six carbapenem-resistant pathogens - a critical genotype-phenotype analysis 2018 Ingår i: Microbial Genomics. - : Microbiology Society. - 2057-5858. ; 4:11 Tidskriftsartikel (refereegranskat)abstract Carbapenem resistance is a rapidly growing threat to our ability to treat refractory bacterial infections. To understand how carbapenem resistance is mobilized and spread between pathogens, it is important to study the genetic context of the underlying resistance mechanisms. In this study, the resistomes of six clinical carbapenem-resistant isolates of five different species - Acinetobacter baumannii, Escherichia colt, two Klebsiella pneumoniae, Proteus mirabilis and Pseudomonas aeruginosa - were characterized using whole genome sequencing. All Enterobacteriaceae isolates and the A. baumannii isolate had acquired a large number of antimicrobial resistance genes (7-18 different genes per isolate), including the following encoding carbapenemases: bla(KPC-2), bla(OXA-48), bla(OXA-72), bla(NDM-1), bla(NDm-7) and bla(VIM-1). In addition, a novel version of bla(SHv) was discovered. Four new resistance plasmids were identified and their fully assembled sequences were verified using optical DNA mapping. Most of the resistance genes were colocalized on these and other plasmids, suggesting a risk for coselection. In contrast, five out of six carbapenemase genes were present on plasmids with no or few other resistance genes. The expected level of resistance - based on acquired resistance determinants - was concordant with measured levels in most cases. There were, however, several important discrepancies for four of the six isolates concerning multiple classes of antibiotics. In conclusion, our results further elucidate the diversity of carbapenemases, their mechanisms of horizontal transfer and possible patterns of co-selection. The study also emphasizes the difficulty of using whole genome sequencing for antimicrobial susceptibility testing of pathogens with complex genotypes.
43.	Khodadad, Davood, 1985-, et al. (författare) Optimized breath detection algorithm in electrical impedance tomography 2018 Ingår i: Physiological Measurement. - : IOP Publishing. - 0967-3334 .- 1361-6579. ; 39:9 Tidskriftsartikel (refereegranskat)abstract Objective: This paper defines a method for optimizing the breath delineation algorithms used in electrical impedance tomography (EIT). In lung EIT the identification of the breath phases is central for generating tidal impedance variation images, subsequent data analysis and clinical evaluation. The optimisation of these algorithms is particularly important in neonatal care since the existing breath detectors developed for adults may give insufficient reliability in neonates due to their very irregular breathing pattern.Approach: Our approach is generic in the sense that it relies on the definition of a gold standard and the associated definition of detector sensitivity and specificity, an optimisation criterion and a set of detector parameters to be investigated. The gold standard has been defined by 11 clinicians with previous experience with EIT and the performance of our approach is described and validated using a neonatal EIT dataset acquired within the EU-funded CRADL project.Main results: Three different algorithms are proposed that improve the breath detector performance by adding conditions on (1) maximum tidal breath rate obtained from zero-crossings of the EIT breathing signal, (2) minimum tidal impedance amplitude and (3) minimum tidal breath rate obtained from time-frequency analysis. As a baseline a zero-crossing algorithm has been used with some default parameters based on the Swisstom EIT device.Significance: Based on the gold standard, the most crucial parameters of the proposed algorithms are optimised by using a simple exhaustive search and a weighted metric defined in connection with the receiver operating characterics. This provides a practical way to achieve any desirable trade-off between the sensitivity and the specificity of the detectors.
44.	Krog, Jens, et al. (författare) Photophysical image analysis : Unsupervised probabilistic thresholding for images from electron-multiplying charge-coupled devices 2024 Ingår i: PLoS ONE. - 1932-6203. ; 19:4, s. 0300122-0300122 Tidskriftsartikel (refereegranskat)abstract We introduce the concept photophysical image analysis (PIA) and an associated pipeline for unsupervised probabilistic image thresholding for images recorded by electron-multiplying charge-coupled device (EMCCD) cameras. We base our approach on a closed-form analytic expression for the characteristic function (Fourier-transform of the probability mass function) for the image counts recorded in an EMCCD camera, which takes into account both stochasticity in the arrival of photons at the imaging camera and subsequent noise induced by the detection system of the camera. The only assumption in our method is that the background photon arrival to the imaging system is described by a stationary Poisson process (we make no assumption about the photon statistics for the signal). We estimate the background photon statistics parameter, λbg, from an image which contains both background and signal pixels by use of a novel truncated fit procedure with an automatically determined image count threshold. Prior to this, the camera noise model parameters are estimated using a calibration step. Utilizing the estimates for the camera parameters and λbg, we then introduce a probabilistic thresholding method, where, for the first time, the fraction of misclassified pixels can be determined a priori for a general image in an unsupervised way. We use synthetic images to validate our a priori estimates and to benchmark against the Otsu method, which is a popular unsupervised non-probabilistic image thresholding method (no a priori estimates for the error rates are provided). For completeness, we lastly present a simple heuristic general-purpose segmentation method based on the thresholding results, which we apply to segmentation of synthetic images and experimental images of fluorescent beads and lung cell nuclei. Our publicly available software opens up for fully automated, unsupervised, probabilistic photophysical image analysis.
45.	Kumar Bikarolla, Santosh, 1985, et al. (författare) Optical DNA Mapping Combined with Cas9-Targeted Resistance Gene Identification for Rapid Tracking of Resistance Plasmids in a Neonatal Intensive Care Unit Outbreak 2019 Ingår i: mBio. - : AMER SOC MICROBIOLOGY. - 2161-2129 .- 2150-7511. ; 10:4 Tidskriftsartikel (refereegranskat)abstract The global spread of antibiotic resistance among Enterobacteriaceae is largely due to multidrug resistance plasmids that can transfer between different bacterial strains and species. Horizontal gene transfer of resistance plasmids can complicate hospital outbreaks and cause problems in epidemiological tracing, since tracing is usually based on bacterial clonality. We have developed a method, based on optical DNA mapping combined with Cas9-assisted identification of resistance genes, which is used here to characterize plasmids during an extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae outbreak at a Swedish neonatal intensive care unit. The outbreak included 17 neonates initially colonized with ESBL-producing Klebsiella pneumoniae (ESBL-KP), some of which were found to carry additional ESBL-producing Escherichia coli (ESBL-EC) in follow-up samples. We demonstrate that all ESBL-KP isolates contained two plasmids with the blaCTX-M-15 gene located on the smaller one (~80 kbp). The same ESBL-KP clone was present in follow-up samples for up to 2 years in some patients, and the plasmid carrying the blaCTX-M-15 gene was stable throughout this time period. However, extensive genetic rearrangements within the second plasmid were observed in the optical DNA maps for several of the ESBL-KP isolates. Optical mapping also demonstrated that even though other bacterial clones and species carrying blaCTX-M group 1 genes were found in some neonates, no transfer of resistance plasmids had occurred. The data instead pointed toward unrelated acquisition of ESBL-producing Enterobacteriaceae (EPE). In addition to revealing important information about the specific outbreak, the method presented is a promising tool for surveillance and infection control in clinical settings.IMPORTANCE This study presents how a novel method, based on visualizing single plasmids using sequence-specific fluorescent labeling, could be used to analyze the genetic dynamics of an outbreak of resistant bacteria in a neonatal intensive care unit at a Swedish hospital. Plasmids are a central reason for the rapid global spread of bacterial resistance to antibiotics. In a single experimental procedure, this method replaces many traditional plasmid analysis techniques that together provide limited details and are slow to perform. The method is much faster than long-read whole-genome sequencing and offers direct genetic comparison of patient samples. We could conclude that no transfer of resistance plasmids had occurred between different bacteria during the outbreak and that secondary cases of ESBL-producing Enterobacteriaceae carriage were instead likely due to influx of new strains. We believe that the method offers potential in improving surveillance and infection control of resistant bacteria in hospitals.
46.	Laland, Kevin N, et al. (författare) The extended evolutionary synthesis: its structure, assumptions and predictions. 2015 Ingår i: Royal Society of London. Proceedings B. Biological Sciences. - : The Royal Society. - 1471-2954. ; 282:1813 Forskningsöversikt (refereegranskat)abstract Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways-one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the 'extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism-environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology.
47.	Lange, Tobias J., et al. (författare) Four-strata risk assessment in patients with pulmonary arterial hypertension treated with selexipag in real-world settings (EXPOSURE study) 2024 Ingår i: Advances in Therapy. - : Springer Nature. - 0741-238X .- 1865-8652. Tidskriftsartikel (refereegranskat)abstract Introduction: Risk assessment can aid management of pulmonary arterial hypertension (PAH) and clinical decision-making. This analysis describes characteristics, treatment patterns and outcomes of patients with PAH, categorised by risk status at time of treatment escalation with selexipag in clinical settings.Methods: Patients initiating selexipag in the ongoing multicentre, prospective EXPOSURE (EUPAS19085) study were grouped as low, intermediate-low, intermediate-high or high risk of 1-year mortality according to the ESC/ERS 4-strata method.Results: As of November 2022, 77% (535/698) of patients initiating selexipag had data allowing for risk calculation; 14% (N = 76) were low, 31% (N = 168) intermediate-low, 34% (N = 182) intermediate-high and 20% (N = 109) high risk of 1-year mortality. Overall, patients were predominantly female (71%), with idiopathic/heritable PAH (56%) or PAH associated with connective tissue disease (CTD-PAH; 27%), median age of 60 years and prevalent (2 years) disease. From low to high risk, proportion of CTD-PAH and age increased (from 12%–40% and 46–68 years, respectively); time from diagnosis decreased and presence of cardiovascular risk factors increased. Most patients across risk groups (74–81%) initiated selexipag as part of triple oral combination therapy. Overall median (Q1, Q3) selexipag exposure duration was 10.1 (3.5, 24.1) months. Proportions of hospitalised patients increased with increasing risk group (16–42% from low to high, respectively); more hospitalisations were PAH-related for the high risk (71%) versus other risk groups (47–54%). Kaplan–Meier survival estimates were 98%, 98%, 93% and 80% at 1-year and 98%, 92%, 81% and 67% at 2-years, from low to high risk, respectively.Conclusions: In clinical settings, selexipag is initiated across all risk groups, predominantly as triple therapy. Only 45% of patients being at low/intermediate-low risk at selexipag initiation suggests an opportunity for more frequent patient monitoring and earlier treatment escalation, given that 4-strata risk assessment was prognostic for hospitalisations and survival in this contemporary PAH cohort. A graphical abstract is available with this article. Graphical Abstract: (Figure presented.)
48.	Laughlin, Ronald J, et al. (författare) Effect of acetate on soil respiration, N2O emissions and gross N transformations related to fungi and bacteria in a grassland soil 2009 Ingår i: Applied Soil Ecology. ; 42, s. 25-30 Tidskriftsartikel (refereegranskat)abstract Application of organic carbon to grassland in the form of manure or cattle slurry during the growing season is a normal agricultural practice. Under enhanced organic C supply changes in the grassland soil’s internal N cycling and in the microbial community are expected, in particular, the fungi–bacteria ratio. Here we present novel results from a 15N tracing study which aimed to investigate the role of fungi and bacteria in N transformations under enhanced organic C supply. We applied 15N labelled fertiliser to soil in a laboratory incubation with and without acetate addition. Moreover, we used specific microbial inhibitors to selectively inhibit either fungi or bacteria. The data from the incubation were used to calculate gross N transformation rates via 15N tracing models based on Monte Carlo sampling techniques. Our results show that fungi are the predominant organisms that carry out N transformations in a temperate grassland soil. Under enhanced organic C supply, the stimulation of the mineralization – immobilization – turnover and heterotrophic nitrification was predominantly related to fungal activity, indicating that fungi may play an increasingly important role in soils with an enhanced C supply. In addition, we showed that fungi were the dominant organisms for N2O production. Increased fungal activity under enhanced organic C supply may therefore increase N2O emissions from soil and have environmental consequences.
49.	Liens, Alethea, et al. (författare) Phase transformation induces plasticity with negligible damage in ceria-stabilized zirconia-based ceramics 2020 Ingår i: Acta Materialia. - : Acta Materialia Inc. - 1359-6454 .- 1873-2453. ; 183, s. 261-273 Tidskriftsartikel (refereegranskat)abstract Ceramics and their composites are in general brittle materials because they are predominantly made up of ionic and covalent bonds that avoid dislocation motion at room temperature. However, a remarkable ductile behavior has been observed on newly developed 11 mol.% ceria-stabilized zirconia (11Ce-TZP) composite containing fine alumina (8 vol.% Al2O3) and elongated strontium hexa-aluminate (8 vol.% SrAl12O19) grains. The as-synthesized composite also has shown full resistance to Low Temperature Degradation (LTD), relatively high strength and exceptionally high Weibull modulus, allowing its use in a broader range of biomedical applications. In this study, to deepen the understanding of plastic deformation in Ce-TZP based composites that could soon be used for manufacturing dental implants, different mechanical tests were applied on the material, followed by complete microstructural characterization. Distinct from pure Ce-TZP material or other zirconia-based ceramics developed in the past, the material here studied can be permanently strained without affecting the Young modulus, indicating that the ductile response of tested samples cannot be associated to damage occurrence. This ductility is related to the stress-induced tetragonal to monoclinic (t-m) zirconia phase transformation, analogue to Transformation-Induced Plasticity (TRIP) steels, where retained austenite is transformed to martensite. The aim of this study is to corroborate if the observed plasticity can be associated exclusively to the zirconia t-m phase transformation, or also to microcraking induced by the transformation. The t-m transformed-zones produced after bending and biaxial tests were examined by X-ray refraction and SEM/TEM coupled with Raman. The results revealed that the observed elastic-plastic behavior occurs without extensive microcracking, confirming a purely elastic-plastic behavior driven by the phase transformation (absence of damage).
50.	Ludwig, Sebastian, et al. (författare) Transcatheter Mitral Valve Replacement versus Medical Therapy for Secondary Mitral Regurgitation: A Propensity Score-Matched Comparison. 2023 Ingår i: Circulation. Cardiovascular interventions. - 1941-7632. ; 16:6 Tidskriftsartikel (refereegranskat)abstract Background: Transcatheter mitral valve replacement (TMVR) is an emerging therapeutic alternative for patients with secondary mitral regurgitation (MR). Outcomes of TMVR versus guideline-directed medical therapy (GDMT) have not been investigated for this population. This study aimed to compare clinical outcomes of patients with secondary MR undergoing TMVR versus GDMT alone. Methods: The CHOICE-MI registry included patients with MR undergoing TMVR using dedicated devices. Patients with MR etiologies other than secondary MR were excluded. Patients treated with GDMT alone were derived from the control arm of the COAPT trial. We compared outcomes between the TMVR and GDMT groups, using propensity score (PS)-matching to adjust for baseline differences. Results: After PS-matching, 97 patient pairs undergoing TMVR (72.9±8.7 years, 60.8% male, transapical access 91.8%) versus GDMT (73.1±11.0 years, 59.8% male) were compared. At 1 and 2 years, residual MR was ≤1+ in all patients of the TMVR group compared to 6.9% and 7.7%, respectively, in those receiving GDMT alone (both p<0.001). The 2-year rate of HF hospitalization was significantly lower in the TMVR group (32.8% vs. 54.4%, HR 0.59, 95% CI 0.35-0.99; p=0.04). Among survivors, a higher proportion of patients were in NYHA functional class I or II in the TMVR group at 1 year (78.2% vs. 59.7%, p=0.03) and at 2 years (77.8% vs. 53.2%, p=0.09). Two-year mortality was similar in the two groups (TMVR vs. GDMT, 36.8% vs. 40.8%, HR 1.01, 95% CI 0.62-1.64; p=0.98). Conclusions: In this observational comparison, over 2-year follow-up, TMVR using mostly transapical devices in patients with secondary MR was associated with significant reduction of MR, symptomatic improvement, less frequent hospitalizations for HF and similar mortality compared with GDMT.

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