| 51. |
- Galicher, R., et al.
(författare)
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Astrometric and photometric accuracies in high contrast imaging : The SPHERE speckle calibration tool (SpeCal)
- 2018
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 615
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Tidskriftsartikel (refereegranskat)abstract
- Context. The consortium of the Spectro-Polarimetric High-contrast Exoplanet REsearch installed at the Very Large Telescope (SPHERE/VLT) has been operating its guaranteed observation time (260 nights over five years) since February 2015. The main part of this time (200 nights) is dedicated to the detection and characterization of young and giant exoplanets on wide orbits. Aims. The large amount of data must be uniformly processed so that accurate and homogeneous measurements of photometry and astrometry can be obtained for any source in the field. Methods. To complement the European Southern Observatory pipeline, the SPHERE consortium developed a dedicated piece of software to process the data. First, the software corrects for instrumental artifacts. Then, it uses the speckle calibration tool (SpeCal) to minimize the stellar light halo that prevents us from detecting faint sources like exoplanets or circumstellar disks. SpeCal is meant to extract the astrometry and photometry of detected point-like sources (exoplanets, brown dwarfs, or background sources). SpeCal was intensively tested to ensure the consistency of all reduced images (cADI, Loci, TLoci, PCA, and others) for any SPHERE observing strategy (ADI, SDI, ASDI as well as the accuracy of the astrometry and photometry of detected point-like sources. Results. SpeCal is robust, user friendly, and efficient at detecting and characterizing point-like sources in high contrast images. It is used to process all SPHERE data systematically, and its outputs have been used for most of the SPHERE consortium papers to date. SpeCal is also a useful framework to compare different algorithms using various sets of data (different observing modes and conditions). Finally, our tests show that the extracted astrometry and photometry are accurate and not biased.
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| 52. |
- Garufi, A., et al.
(författare)
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The SPHERE view of the Taurus star-forming region : The full census of planet-forming disks with GTO and DESTINYS programs
- 2024
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Ingår i: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 685
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Tidskriftsartikel (refereegranskat)abstract
- The sample of planet-forming disks observed by high-contrast imaging campaigns over the last decade is mature enough to enable the demographical analysis of individual star-forming regions. We present the full census of Taurus sources with VLT/SPHERE polarimetric images available. The whole sample sums up to 43 targets (of which 31 have not been previously published) corresponding to one-fifth of the Class II population in Taurus and about half of such objects that are observable. A large fraction of the sample is apparently made up of isolated faint disks (equally divided between small and large self-shadowed disks). Ambient signal is visible in about one-third of the sample. This probes the interaction with the environment and with companions or the outflow activity of the system. The central portion of the Taurus region almost exclusively hosts faint disks, while the periphery also hosts bright disks interacting with their surroundings. The few bright disks are found around apparently older stars. The overall picture is that the Taurus region is in an early evolutionary stage of planet formation. Yet, some objects are discussed individually, as in an intermediate or exceptional stage of the disk evolution. This census provides a first benchmark for the comparison of the disk populations in different star forming regions.
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| 53. |
- Geraldine Guex, Anne, et al.
(författare)
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Controlling pH by electronic ion pumps to fight fibrosis
- 2021
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Ingår i: Applied Materials Today. - : Elsevier. - 2352-9407. ; 22
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Tidskriftsartikel (refereegranskat)abstract
- Fibrosis and scar formation is a medical condition observed under various circumstances, ranging from skin wound healing to cardiac deterioration after myocardial infarction. Among other complex interdependent phases during wound healing, fibrosis is associated with an increased fibroblast to myofibroblast transition. A common hypothesis is that decreasing the pH of non-healing, alkaline wounds to a pH range of 6.0 to 6.5 increases healing rates. A new material-based strategy to change the pH by use of electronic ion pumps is here proposed. In contrast to passive acidic wound dressings limited by non-controlled delivery kinetics, the unique electronic ion pump design and operation enables a continuous regulation of pH by H+ delivery over prolonged durations. In an in vitro model, fibroblast to myofibroblast differentiation is attenuated by lowering the physiological pH to an acidic regime of 6.62 +/- 0.06. Compared to differentiated myofibroblasts in media at pH 7.4, gene and protein expression of fibrosis relevant markers alpha-smooth muscle actin and collagen 1 is significantly reduced. In conclusion, myofibroblast differentiation can be steered by controlling the pH of the cellular microenvironment by use of the electronic ion pump technology as new bioelectronic drug delivery devices. This technology opens up new therapeutic avenues to induce scar-free wound healing. (C) 2021 The Authors. Published by Elsevier Ltd.
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| 54. |
- Ginski, C., et al.
(författare)
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An extended scattered light disk around AT Pyx. Possible planet formation in a cometary globule
- 2022
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 662
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Tidskriftsartikel (refereegranskat)abstract
- Aims. To understand how the multitude of planetary systems that have been discovered come to be, we need to study systems at different evolutionary stages, with different central stars but also in different environments. The most challenging environment for planet formation may be the harsh UV radiation field of nearby massive stars which quickly erodes disks by external photo-evaporation. We observed the AT Pyx system, located in the head of a cometary globule in the Gum Nebula, to search for signs of ongoing planet formation.Methods. We used the extreme adaptive optics imager VLT/SPHERE in Dual Beam Polarization Imaging Mode in H-band as well as in IRDIFS Extended mode (K12-band imaging and Y-H integral field spectroscopy) to observe AT Pyx in polarized light and total intensity. Additionally, we employed VLT/NACO to observe the system in the L-band.Results. We resolve the disk around AT Pyx for the first time in scattered light across multiple wavelengths in polarized light and total intensity. We find an extended (≥126 au) disk, with an intermediate inclination of between 35° and 42°. The disk shows a complex substructure and we identify two or possibly three spiral-like features. Depending on the precise geometry of the disk (which we cannot unambiguously infer from our data), the disk may be eccentric with an eccentricity of ~0.16 or partially self-shadowed. The spiral features and possible eccentricity are both consistent with signatures of an embedded gas giant planet with a mass of ~1 MJup. Our own observations can rule out brown dwarf companions embedded in the resolved disk, but are nevertheless not sensitive enough to confirm or rule out the presence of a gas giant.Conclusions. AT Pyx is the first disk to be spatially resolved in a cometary globule in the Gum Nebula. By comparison with disks in the Orion Nebula Cluster we note that the extension of the disk may be exceptional for this environment if the external UV radiation field is indeed comparable to other cometary globules in the region. The signposts of ongoing planet formation are intriguing and need to be followed up with either higher sensitivity or at different wavelengths.
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| 55. |
- Gispert, Suzana, et al.
(författare)
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The modulation of Amyotrophic Lateral Sclerosis risk by Ataxin-2 intermediate polyglutamine expansions is a specific effect
- 2012
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Ingår i: Neurobiology of Disease. - : Elsevier. - 0969-9961 .- 1095-953X. ; 45:1, s. 356-361
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Tidskriftsartikel (refereegranskat)abstract
- Full expansions of the polyglutamine domain (polyQ >= 34) within the polysome-associated protein ataxin-2 (ATXN2) are the cause of a multi-system neurodegenerative disorder, which usually presents as a Spino-Cerebellar Ataxia and is therefore known as SCA2, but may rarely manifest as Levodopa-responsive Parkinson syndrome or as motor neuron disease. Intermediate expansions (27 <= polyQ <= 33) were reported to modify the risk of Amyotrophic Lateral Sclerosis (ALS). We have now tested the reproducibility and the specificity of this observation. In 559 independent ALS patients from Central Europe, the association of ATXN2 expansions (30 <= polyQ <= 35) with ALS was highly significant. The study of 1490 patients with Parkinson's disease (PD) showed an enrichment of ATXN2 alleles 27/28 in a subgroup with familial cases, but the overall risk of sporadic PD was unchanged. No association was found between polyQ expansions in Ataxin-3 (ATXN3) and ALS risk. These data indicate a specific interaction between ATXN2 expansions and the causes of ALS, possibly through altered RNA-processing as a common pathogenic factor. (C) 2011 Elsevier Inc. All rights reserved.
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| 56. |
- Heiss, Maximilian, et al.
(författare)
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Endothelial cell spheroids as a versatile tool to study angiogenesis in vitro
- 2015
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Ingår i: The FASEB Journal. - : Wiley. - 0892-6638 .- 1530-6860. ; 29:7, s. 3076-3084
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Tidskriftsartikel (refereegranskat)abstract
- Given the need for robust and cost-efficient in vitro models to study angiogenesis and reproducibly analyze potential pro-and antiangiogenic compounds in preclinical studies, we developed a 3-dimensional in vitro angiogenesis assay that is based on collagen gel-embedded, size-defined spheroids generated from cultured human umbilical vein endothelial cells (HUVECs). Despite its wide distribution, limitations, sensitivity, robustness, and improvements, the capacity of this assay for functional screening purposes has not been elucidated thus far. By using time-lapse video microscopy, we show that tip cells lead the formation of capillary-like and partially lumenized sprouts originating from the spheroids. Angiogenic sprouting from spheroids generated from 5 different primary cultured human endothelial cell types was induced by physiologic concentrations of vascular endothelial cell growth factor 165. Based on this assay system, we determined the capacity of 880 approved drugs to interfere with or boost angiogenic sprouting, thereby assessing their putative angiogenesis-related side effects or novel applications. However, although this assay allowed for a rapid and reproducible determination of functional IC50 values of individual compounds, the sprouting results were partially affected by the HUVEC passage number and donor variability. To overcome this limitation, immortalized HUVECs (iHUVECs) showing a more homogenous response in terms of proliferation and sprouting over multiple population doublings were used in the course of this study. Collectively, the spheroid-based angiogenesis assay provides a sensitive and versatile tool to study the impact of pro-and antiangiogenic determinants on multiple steps of the angiogenic cascade. It is compatible with different endothelial cell types and allows use of iHUVECs to improve its overall robustness.
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| 57. |
- Hillberg, Emil, et al.
(författare)
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Active Network Management for All : ANM4L a collaborative research project
- 2020
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Developments of the power system are driven by the need to decrease the environmental footprint, to meet international climate goals, pushing for fossil‐free energy system. The transition towards clean energy will require power systems to adapt on a global scale with significant investments needed in fossil‐free electricity generation and transport. Renewable Energy Sources (RES) play an increasingly important role in the power system and may become the dominant sources of electricity. Significant RES are integrated in distribution grids globally, resulting in an increased need for distribution grids to perform new and complex tasks necessary for continued grid stability. The rapidity of small‐scale investments calls for agile, alternative grid development solutions. This agility is furthermore necessary to meet challenges arising from demand scenarios encompassing intermittent renewables along with electrification of transport and heat sectors. New technologies and markets are emerging to provide flexibility in consumption, generation, and power transfer capacity. Active Network Management (ANM) solutions provides alternative methods for planning and operation of the power system, through monitoring and control of multiple grid assets. This paper presents an overview of the ongoing project ANM4L, where a toolbox will be developed to support operation and planning of distribution grids.The project ANM4L (Active network management for all - anm4l.eu), will develop and demonstrate innovative ANM solutions for increasing integration of distributed generation in electricity distribution systems. ANM solutions will consider management of active and reactive power to avoid overload situations and maintain voltage limits. The goal is to decrease the need of curtailment of renewable energy, theoretically enabling further integration of distributed generation potentially even above the current design limitations of the electricity network. Core research and development activities of the ANM4L project include development of: ANM methods for local energy systems. Economic considerations to provide decision support. A toolbox to support the planning and operation. The toolbox, methods and business models for ANM will be demonstrated in real life distribution grids in both Sweden and Hungary. Furthermore, the project will consider the replicability and scalability necessary for these ANM solutions to be applied across the EU.
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| 58. |
- Hop, Paul J., et al.
(författare)
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Genome-wide study of DNA methylation shows alterations in metabolic, inflammatory, and cholesterol pathways in ALS
- 2022
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Ingår i: Science Translational Medicine. - : American Association for the Advancement of Science. - 1946-6234 .- 1946-6242. ; 14:633
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Tidskriftsartikel (refereegranskat)abstract
- Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with an estimated heritability between 40 and 50%. DNA methylation patterns can serve as proxies of (past) exposures and disease progression, as well as providing a potential mechanism that mediates genetic or environmental risk. Here, we present a blood-based epigenome-wide association study meta-analysis in 9706 samples passing stringent quality control (6763 patients, 2943 controls). We identified a total of 45 differentially methylated positions (DMPs) annotated to 42 genes, which are enriched for pathways and traits related to metabolism, cholesterol biosynthesis, and immunity. We then tested 39 DNA methylation-based proxies of putative ALS risk factors and found that high-density lipoprotein cholesterol, body mass index, white blood cell proportions, and alcohol intake were independently associated with ALS. Integration of these results with our latest genome-wide association study showed that cholesterol biosynthesis was potentially causally related to ALS. Last, DNA methylation at several DMPs and blood cell proportion estimates derived from DNA methylation data were associated with survival rate in patients, suggesting that they might represent indicators of underlying disease processes potentially amenable to therapeutic interventions.
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| 59. |
- Huhn, Stefanie, et al.
(författare)
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Coding variants in NOD-like receptors : An association study on risk and survival of colorectal cancer
- 2018
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 13:6
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Tidskriftsartikel (refereegranskat)abstract
- Nod-like receptors (NLRs) are important innate pattern recognition receptors and regulators of inflammation or play a role during development. We systematically analysed 41 non-synonymous single nucleotide polymorphisms (SNPs) in 21 NLR genes in a Czech discovery cohort of sporadic colorectal cancer (CRC) (1237 cases, 787 controls) for their association with CRC risk and survival. Five SNPs were found to be associated with CRC risk and eight with survival at 5% significance level. In a replication analysis using data of two large genome-wide association studies (GWASs) from Germany (DACHS: 1798 cases and 1810 controls) and Scotland (2210 cases and 9350 controls) the associations found in the Czech discovery set were not confirmed. However, expression analysis in human gut-related tissues and immune cells revealed that the NLRs associated with CRC risk or survival in the discovery set were expressed in primary human colon or rectum cells, CRC tissue and/or cell lines, providing preliminary evidence for a potential involvement of NLRs in general in CRC development and/or progression. Most interesting was the finding that the enigmatic development-related NLRP5 (also known as MATER) was not expressed in normal colon tissue but in colon cancer tissue and cell lines. Future studies may show whether regulatory variants instead of coding variants might affect the expression of NLRs and contribute to CRC risk and survival.
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| 60. |
- Jimenez-del-Toro, Oscar, et al.
(författare)
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Cloud-Based Evaluation of Anatomical Structure Segmentation and Landmark Detection Algorithms : VISCERAL Anatomy Benchmarks
- 2016
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Ingår i: IEEE Transactions on Medical Imaging. - : Institute of Electrical and Electronics Engineers (IEEE). - 0278-0062 .- 1558-254X. ; 35:11, s. 2459-2475
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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.
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