| 1. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 2. |
- Weber, Sebastian, et al.
(författare)
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Evolution of Hierarchically Porous Nickel Alumina Catalysts Studied by X-Ray Ptychography
- 2022
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Ingår i: Advanced science (Weinheim, Baden-Wurttemberg, Germany). - : Wiley. - 2198-3844. ; 9:8, s. 2105432-2105432
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Tidskriftsartikel (refereegranskat)abstract
- The synthesis of hierarchically porous materials usually requires complex experimental procedures, often based around extensive trial and error approaches. One common synthesis strategy is the sol-gel method, although the relation between synthesis parameters, material structure and function has not been widely explored. Here, in situ 2D hard X-ray ptychography (XRP) and 3D ptychographic X-ray computed tomography (PXCT) are applied to monitor the development of hierarchical porosity in Ni/Al2 O3 and Al2 O3 catalysts with connected meso- and macropore networks. In situ XRP allows to follow textural changes of a dried gel Ni/Al2 O3 sample as a function of temperature during calcination, activation and CO2 methanation reaction. Complementary PXCT studies on dried gel particles of Ni/Al2 O3 and Al2 O3 provide quantitative information on pore structure, size distribution, and shape with 3D spatial resolution approaching 50 nm, while identical particles are imaged ex situ before and after calcination. The X-ray imaging results are correlated with N2 -sorption, Hg porosimetry and He pycnometry pore characterization. Hard X-ray nanotomography is highlighted to derive fine structural details including tortuosity, branching nodes, and closed pores, which are relevant in understanding transport phenomena during chemical reactions. XRP and PXCT are enabling technologies to understand complex synthesis pathways of porous materials.
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| 3. |
- Achilles, Silvio, et al.
(författare)
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GPU-Accelerated Coupled Ptychographic Tomography
- 2022
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Ingår i: Developments in X-Ray Tomography XIV. - : SPIE. - 1996-756X .- 0277-786X. - 9781510654686 ; 12242
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Konferensbidrag (refereegranskat)abstract
- Scanning coherent X-ray microscopy (ptychography) has gained considerable interest during the last decade since the performance of this indirect imaging technique does not necessarily rely on the quality of the X-ray optics and, in principle, can achieve highest spatial resolution in X-ray imaging. The method can be easily extended to 3D by adding standard tomographic reconstruction schemes. However, the tomographic reconstruction is often applied in a subsequent step using a sequence of aligned ptychographic 2D projections. In this contribution, we outline current developments of a GPU-accelerated framework for direct 3D ptychography, coupling 2D ptychography and tomography. The program utilizes a custom GPU-accelerated framework for ptychography that offers three distinct ptychographic reconstruction algorithms. The tomographic reconstruction runs simultaneously and uses numerical routines of the ASTRA Toolbox. This parallel-computing approach results in a high performance increase considerably reducing the reconstruction time of 3D ptychographic datasets.
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| 4. |
- Benzi, Federico, et al.
(författare)
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Transient structural and catalytic behaviour of Pt-particles probed by operando spectroscopy during a realistic driving cycle
- 2017
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Ingår i: Catalysis Science & Technology. - : Royal Society of Chemistry (RSC). - 2044-4753 .- 2044-4761. ; 7:18, s. 3999-4006
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Tidskriftsartikel (refereegranskat)abstract
- Pt-based diesel oxidation catalysts were investigated for CO oxidation activity under rapid transient temperature conditions based on a realistic driving cycle, which is presently a focal point in exhaust gas aftertreatment. Experiments were performed in a microreactor setup allowing rapid heating/cooling coupled with operando Turbo X-ray absorption spectroscopy (T-XAS) and on-line product analysis by mass spectrometry. Significant differences were observed in catalyst structure and performance depending on the temperature ramp rate. Particularly for Pt/Al2O3, the Pt oxidation state followed a dynamic hysteresis profile during CO oxidation light-off and light-out. In contrast, in Pt-CeO2/Al2O3, ceria acted as an oxygen storage buffer, reducing the width of the Pt oxidation/reduction hysteresis loop as a function of the temperature ramp rate. Ceria also supplied oxygen to the Pt surface, helping to maintain high activity during cooling down and at lower temperatures during transient conditions. This study shows the potential insights into the reaction mechanism available when considering transient temperature as an experimental condition during operando spectroscopic studies in exhaust gas catalysis. The current method is applicable to virtually any rapid transient temperature driving cycle.
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| 5. |
- Berthenet, Elvire, et al.
(författare)
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A GWAS on Helicobacter pylori strains points to genetic variants associated with gastric cancer risk
- 2018
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Ingår i: BMC Biology. - : BioMed Central. - 1741-7007. ; 16:1
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND:Helicobacter pylori are stomach-dwelling bacteria that are present in about 50% of the global population. Infection is asymptomatic in most cases, but it has been associated with gastritis, gastric ulcers and gastric cancer. Epidemiological evidence shows that progression to cancer depends upon the host and pathogen factors, but questions remain about why cancer phenotypes develop in a minority of infected people. Here, we use comparative genomics approaches to understand how genetic variation amongst bacterial strains influences disease progression.RESULTS:We performed a genome-wide association study (GWAS) on 173 H. pylori isolates from the European population (hpEurope) with known disease aetiology, including 49 from individuals with gastric cancer. We identified SNPs and genes that differed in frequency between isolates from patients with gastric cancer and those with gastritis. The gastric cancer phenotype was associated with the presence of babA and genes in the cag pathogenicity island, one of the major virulence determinants of H. pylori, as well as non-synonymous variations in several less well-studied genes. We devised a simple risk score based on the risk level of associated elements present, which has the potential to identify strains that are likely to cause cancer but will require refinement and validation.CONCLUSION:There are a number of challenges to applying GWAS to bacterial infections, including the difficulty of obtaining matched controls, multiple strain colonization and the possibility that causative strains may not be present when disease is detected. Our results demonstrate that bacterial factors have a sufficiently strong influence on disease progression that even a small-scale GWAS can identify them. Therefore, H. pylori GWAS can elucidate mechanistic pathways to disease and guide clinical treatment options, including for asymptomatic carriers.
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| 6. |
- Henderson, Neil C., et al.
(författare)
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Targeting of alpha(v) integrin identifies a core molecular pathway that regulates fibrosis in several organs
- 2013
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Ingår i: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 19:12, s. 1617-1624
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Tidskriftsartikel (refereegranskat)abstract
- Myofibroblasts are the major source of extracellular matrix components that accumulate during tissue fibrosis, and hepatic stellate cells (HSCs) are believed to be the major source of myofibroblasts in the liver. To date, robust systems to genetically manipulate these cells have not been developed. We report that Cre under control of the promoter of Pdgfrb (Pdgfrb-Cre) inactivates loxP-flanked genes in mouse HSCs with high efficiency. We used this system to delete the gene encoding alpha(v) integrin subunit because various alpha(v)-containing integrins have been suggested as central mediators of fibrosis in multiple organs. Such depletion protected mice from carbon tetrachloride-induced hepatic fibrosis, whereas global loss of beta(3), beta(5) or beta(6) integrins or conditional loss of beta(8) integrins in HSCs did not. We also found that Pdgfrb-Cre effectively targeted myofibroblasts in multiple organs, and depletion of the alpha(v) integrin subunit using this system was protective in other models of organ fibrosis, including pulmonary and renal fibrosis. Pharmacological blockade of alpha(v)-containing integrins by a small molecule (CWHM 12) attenuated both liver and lung fibrosis, including in a therapeutic manner. These data identify a core pathway that regulates fibrosis and suggest that pharmacological targeting of all alpha(v) integrins may have clinical utility in the treatment of patients with a broad range of fibrotic diseases.
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| 7. |
- Li, Tang, et al.
(författare)
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X-Ray Multibeam Ptychography at up to 20 keV : Nano-Lithography Enhances X-Ray Nano-Imaging
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Ingår i: Advanced Science. - 2198-3844.
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Tidskriftsartikel (refereegranskat)abstract
- Hard X-rays are needed for non-destructive nano-imaging of solid matter. Synchrotron radiation facilities (SRF) provide the highest-quality images with single-digit nm resolution using advanced techniques such as X-ray ptychography. However, the resolution or field of view is ultimately constrained by the available coherent flux. To address this, the beam's incoherent fraction can be exploited using multiple parallel beams in an X-ray multibeam ptychography (MBP) approach. This expands the domain of X-ray ptychography to larger samples or more rapid measurements. Both qualities favor the study of complex composite or functional samples, such as catalysts, energy materials, or electronic devices. The challenge of performing ptychography at high energy and with many parallel beams must be overcome to extract the full advantages for extended samples while minimizing beam attenuation. Here, that challenge is overcome by creating a lens array using cutting-edge laser printing technology and applying it to perform scanning with MBP with up to 12 beams and at photon energies of 13 and 20 keV. This exceeds the measurement limits of conventional hard X-ray ptychography without compromising image quality for various samples: Siemens star test pattern, Ni/Al2O3 catalyst, microchip, and gold nano-crystal clusters.
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| 8. |
- Mageiros, Leonardos, et al.
(författare)
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Genome evolution and the emergence of pathogenicity in avian Escherichia coli
- 2021
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Chickens are the most common birds on Earth and colibacillosis is among the most common diseases affecting them. This major threat to animal welfare and safe sustainable food production is difficult to combat because the etiological agent, avian pathogenic Escherichia coli (APEC), emerges from ubiquitous commensal gut bacteria, with no single virulence gene present in all disease-causing isolates. Here, we address the underlying evolutionary mechanisms of extraintestinal spread and systemic infection in poultry. Combining population scale comparative genomics and pangenome-wide association studies, we compare E. coli from commensal carriage and systemic infections. We identify phylogroup-specific and species-wide genetic elements that are enriched in APEC, including pathogenicity-associated variation in 143 genes that have diverse functions, including genes involved in metabolism, lipopolysaccharide synthesis, heat shock response, antimicrobial resistance and toxicity. We find that horizontal gene transfer spreads pathogenicity elements, allowing divergent clones to cause infection. Finally, a Random Forest model prediction of disease status (carriage vs. disease) identifies pathogenic strains in the emergent ST-117 poultry-associated lineage with 73% accuracy, demonstrating the potential for early identification of emergent APEC in healthy flocks.
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| 9. |
- Santander, Nicolas, et al.
(författare)
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Lack of Flvcr2 impairs brain angiogenesis without affecting the blood-brain barrier
- 2020
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Ingår i: Journal of Clinical Investigation. - 0021-9738 .- 1558-8238. ; 130:8, s. 4055-4068
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Tidskriftsartikel (refereegranskat)abstract
- Fowler syndrome is a rare autosomal recessive brain vascular disorder caused by mutation in FLVCR2 in humans. The disease occurs during a critical period of brain vascular development, is characterized by glomeruloid vasculopathy and hydrocephalus, and is almost invariably prenatally fatal. Here, we sought to gain insights into the process of brain vascularization and the pathogenesis of Fowler syndrome by inactivating Flvcr2 in mice. We showed that Flvcr2 was necessary for angiogenic sprouting in the brain, but surprisingly dispensable for maintaining the blood-brain barrier. Endothelial cells lacking Flvcr2 had altered expression of angiogenic factors, failed to adopt tip cell properties, and displayed reduced sprouting, leading to vascular malformations similar to those seen in humans with Fowler syndrome. Brain hypovascularization was associated with hypoxia and tissue infarction, ultimately causing hydrocephalus and death of mutant animals. Strikingly, despite severe vascular anomalies and brain tissue infarction, the blood-brain barrier was maintained in Flvcr2 mutant mice. Our Fowler syndrome model therefore defined the pathobiology of this disease and provided new insights into brain angiogenesis by showing uncoupling of vessel morphogenesis and blood-brain barrier formation.
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| 10. |
- Schropp, Andreas, et al.
(författare)
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PtyNAMi : Ptychographic nano-analytical microscope
- 2020
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Ingår i: Journal of Applied Crystallography. - 0021-8898. ; 53, s. 957-971
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Tidskriftsartikel (refereegranskat)abstract
- Ptychographic X-ray imaging at the highest spatial resolution requires an optimal experimental environment, providing a high coherent flux, excellent mechanical stability and a low background in the measured data. This requires, for example, a stable performance of all optical components along the entire beam path, high temperature stability, a robust sample and optics tracking system, and a scatter-free environment. This contribution summarizes the efforts along these lines to transform the nanoprobe station on beamline P06 (PETRAIII) into the ptychographic nano-analytical microscope (PtyNAMi).
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| 11. |
- Sikkema, Lisa, et al.
(författare)
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An integrated cell atlas of the lung in health and disease
- 2023
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Ingår i: Nature Medicine. - : Springer Nature. - 1078-8956 .- 1546-170X. ; 29:6, s. 1563-1577
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Tidskriftsartikel (refereegranskat)abstract
- Single-cell technologies have transformed our understanding of human tissues. Yet, studies typically capture only a limited number of donors and disagree on cell type definitions. Integrating many single-cell datasets can address these limitations of individual studies and capture the variability present in the population. Here we present the integrated Human Lung Cell Atlas (HLCA), combining 49 datasets of the human respiratory system into a single atlas spanning over 2.4 million cells from 486 individuals. The HLCA presents a consensus cell type re-annotation with matching marker genes, including annotations of rare and previously undescribed cell types. Leveraging the number and diversity of individuals in the HLCA, we identify gene modules that are associated with demographic covariates such as age, sex and body mass index, as well as gene modules changing expression along the proximal-to-distal axis of the bronchial tree. Mapping new data to the HLCA enables rapid data annotation and interpretation. Using the HLCA as a reference for the study of disease, we identify shared cell states across multiple lung diseases, including SPP1 + profibrotic monocyte-derived macrophages in COVID-19, pulmonary fibrosis and lung carcinoma. Overall, the HLCA serves as an example for the development and use of large-scale, cross-dataset organ atlases within the Human Cell Atlas.
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| 12. |
- Valerie, Nicholas C. K., et al.
(författare)
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NUDT15 Hydrolyzes 6-Thio-DeoxyGTP to Mediate the Anticancer Efficacy of 6-Thioguanine
- 2016
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Ingår i: Cancer Research. - 0008-5472 .- 1538-7445. ; 76:18, s. 5501-5511
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Tidskriftsartikel (refereegranskat)abstract
- Thiopurines are a standard treatment for childhood leukemia, but like all chemotherapeutics, their use is limited by inherent or acquired resistance in patients. Recently, the nucleoside diphosphate hydrolase NUDT15 has received attention on the basis of its ability to hydrolyze the thiopurine effector metabolites 6-thio-deoxyGTP (6-thio-dGTP) and 6-thio-GTP, thereby limiting the efficacy of thiopurines. In particular, increasing evidence suggests an association between the NUDT15 missense variant, R139C, and thiopurine sensitivity. In this study, we elucidated the role of NUDT15 and NUDT15 R139C in thiopurine metabolism. In vitro and cellular results argued that 6-thio-dGTP and 6-thio-GTP are favored substrates for NUDT15, a finding supported by a crystallographic determination of NUDT15 in complex with 6-thio-GMP. We found that NUDT15 R139C mutation did not affect enzymatic activity but instead negatively influenced protein stability, likely due to a loss of supportive intramolecular bonds that caused rapid proteasomal degradation in cells. Mechanistic investigations in cells indicated that NUDT15 ablation potentiated induction of the DNA damage checkpoint and cancer cell death by 6-thioguanine. Taken together, our results defined how NUDT15 limits thiopurine efficacy and how genetic ablation via the R139C missense mutation confers sensitivity to thiopurine treatment in patients.
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| 13. |
- Yang, Xiaogang, et al.
(författare)
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Tomographic reconstruction with a generative adversarial network
- 2020
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Ingår i: Journal of Synchrotron Radiation. - 0909-0495. ; 27, s. 486-493
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Tidskriftsartikel (refereegranskat)abstract
- This paper presents a deep learning algorithm for tomographic reconstruction (GANrec). The algorithm uses a generative adversarial network (GAN) to solve the inverse of the Radon transform directly. It works for independent sinograms without additional training steps. The GAN has been developed to fit the input sinogram with the model sinogram generated from the predicted reconstruction. Good quality reconstructions can be obtained during the minimization of the fitting errors. The reconstruction is a self-Training procedure based on the physics model, instead of on training data. The algorithm showed significant improvements in the reconstruction accuracy, especially for missing-wedge tomography acquired at less than 180° rotational range. It was also validated by reconstructing a missing-wedge X-ray ptychographic tomography (PXCT) data set of a macroporous zeolite particle, for which only 51 projections over 70° could be collected. The GANrec recovered the 3D pore structure with reasonable quality for further analysis. This reconstruction concept can work universally for most of the ill-posed inverse problems if the forward model is well defined, such as phase retrieval of in-line phase-contrast imaging.
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