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| 2. |
- Bott, Lukas Thomas, et al.
(författare)
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Coulomb dissociation of O-16 into He-4 and C-12
- 2023
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Ingår i: NUCLEAR PHYSICS IN ASTROPHYSICS - X, NPA-X 2022. - : EDP Sciences. - 2100-014X. ; 279
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Konferensbidrag (refereegranskat)abstract
- We measured the Coulomb dissociation of O-16 into He-4 and C-12 within the FAIR Phase-0 program at GSI Helmholtzzentrum fur Schwerionenforschung Darmstadt, Germany. From this we will extract the photon dissociation cross section O-16(alpha,gamma)C-12, which is the time reversed reaction to C-12(alpha,gamma)O-16. With this indirect method, we aim to improve on the accuracy of the experimental data at lower energies than measured so far. The expected low cross section for the Coulomb dissociation reaction and close magnetic rigidity of beam and fragments demand a high precision measurement. Hence, new detector systems were built and radical changes to the (RB)-B-3 setup were necessary to cope with the high-intensity O-16 beam. All tracking detectors were designed to let the unreacted O-16 ions pass, while detecting the C-12 and He-4.
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| 3. |
- Ravikumar, Sadhana, et al.
(författare)
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Improved Segmentation of Deep Sulci in Cortical Gray Matter Using a Deep Learning Framework Incorporating Laplace’s Equation
- 2023
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Ingår i: Information Processing in Medical Imaging - 28th International Conference, IPMI 2023, Proceedings. - 1611-3349 .- 0302-9743. - 9783031340475 ; 13939 LNCS, s. 692-704
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Konferensbidrag (refereegranskat)abstract
- When developing tools for automated cortical segmentation, the ability to produce topologically correct segmentations is important in order to compute geometrically valid morphometry measures. In practice, accurate cortical segmentation is challenged by image artifacts and the highly convoluted anatomy of the cortex itself. To address this, we propose a novel deep learning-based cortical segmentation method in which prior knowledge about the geometry of the cortex is incorporated into the network during the training process. We design a loss function which uses the theory of Laplace’s equation applied to the cortex to locally penalize unresolved boundaries between tightly folded sulci. Using an ex vivo MRI dataset of human medial temporal lobe specimens, we demonstrate that our approach outperforms baseline segmentation networks, both quantitatively and qualitatively.
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| 4. |
- Ravikumar, Sadhana, et al.
(författare)
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Unfolding the Medial Temporal Lobe Cortex to Characterize Neurodegeneration Due to Alzheimer’s Disease Pathology Using Ex vivo Imaging
- 2021
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Ingår i: Machine Learning in Clinical Neuroimaging - 4th International Workshop, MLCN 2021, Held in Conjunction with MICCAI 2021, Proceedings. - Cham : Springer International Publishing. - 0302-9743 .- 1611-3349. - 9783030875855 ; 13001 LNCS, s. 3-12
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Konferensbidrag (refereegranskat)abstract
- Neurofibrillary tangle (NFT) pathology in the medial temporal lobe (MTL) is closely linked to neurodegeneration, and is the early pathological change associated with Alzheimer’s Disease (AD). In this work, we investigate the relationship between MTL morphometry features derived from high-resolution ex vivo imaging and histology-based measures of NFT pathology using a topological unfolding framework applied to a dataset of 18 human postmortem MTL specimens. The MTL has a complex 3D topography and exhibits a high degree of inter-subject variability in cortical folding patterns which poses a significant challenge for volumetric registration methods typically used during MRI template construction. By unfolding the MTL cortex, the proposed framework explicitly accounts for the sheet-like geometry of the MTL cortex and provides a two-dimensional reference coordinate space which can be used to implicitly register cortical folding patterns across specimens based on distance along the cortex despite large anatomical variability. Leveraging this framework in a subset of 15 specimens, we characterize the associations between NFTs and morphological features such as cortical thickness and surface curvature and identify regions in the MTL where patterns of atrophy are strongly correlated with NFT pathology.
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| 5. |
- Roh, Hyung S., et al.
(författare)
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Integrating Color Deconvolution Thresholding and Weakly Supervised Learning for Automated Segmentation of Neurofibrillary Tangle and Neuropil Threads
- 2023
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Ingår i: Medical Imaging 2023 : Digital and Computational Pathology - Digital and Computational Pathology. - 1605-7422. - 9781510660472 ; 12471
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Konferensbidrag (refereegranskat)abstract
- Abnormally phosphorylated tau proteins are known to be a major indicator of Alzheimer's Disease (AD) with strong association with memory loss and cognitive decline. Automated generation of pixel-wise accurate neurofibrillary tangles (NFTs) and neuropil threads (NTs) segmentation is a challenging task, due to lack of ground truth segmentation data of these abnormal tau pathology. This problem is most prominent in the case of segmenting NTs, where the small threadlike morphology makes pixel-wise labeling a laborious task and unrealistic for large-scale studies. Lack of ground truth data poses a significant limitation for many learning-based methods to generate accurate segmentations of NFTs and NTs. This work presents an automated pipeline for pixel level segmentation of NFTs and NTs that does not rely on ground truth segmentation data. The pipeline is composed of four main steps: (1) color deconvolution is used to separate histopathology images into staining channels (DAB, Hematoxylin, and Eosin), (2) Otsu's thresholding is used on the DAB stain channel to generate pixel level segmentation of abnormal tau proteins staining, (3) a weakly-supervised learning paradigm (WildCat), using only global descriptors of images, is used to generate density maps of potential regions of NFTs and NTs, and (4) density maps and segmentations are then integrated using connected component analysis to localize NFTs and NTs in the detected tau segmentations. Our results show high global classification accuracy for NFTs (Acc:0.96) and NTs (Acc:0.91), and statistically significant distinctions when evaluating the percent area occupied of the detected NTs relative to expert ratings of NTs severity. Qualitative assessment of the NFTs and NTs results showed accurate pixel-level segmentations of the NFTs, while modest performance for NTs.
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| 6. |
- Absil, Olivier, et al.
(författare)
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An update on the VORTEX project
- 2015
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Ingår i: Techniques and Instrumentation for Detection of Exoplanets VII. - : SPIE.
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Konferensbidrag (refereegranskat)abstract
- In this talk, we will review the on-going activities within the VORTEX teamat the University of Liège and Uppsala University. The VORTEX project aimsto design, manufacture, test, and exploit vector vortex phase masks madeof sub-wavelength gratings (aka the Annular Groove Phase Mask, AGPM)for the direct detection and characterization of extrasolar planets. This talkwill specifically report on the commissioning of several AGPMs on infraredcameras equipping 10-m class telescopes, including the VLT, the LBT andthe Keck. We will describe the in-lab and on-sky performance of the AGPMs,and discuss first scientific observations. We will also report on the lessonslearned from the on-sky operation of our vortices, and discuss ways toimprove their performance. The potential of our coronagraphic devices inthe context of future extremely large telescopes and space missions will alsobe addressed.
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| 7. |
- Absil, Olivier, et al.
(författare)
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The VORTEX project : first results and perspectives
- 2014
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Ingår i: Adaptive Optics Systems IV. - : SPIE. - 9780819496164
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Konferensbidrag (refereegranskat)abstract
- Vortex coronagraphs are among the most promising solutions to perform high contrast imaging at small angular separations from bright stars. They feature a very small inner working angle (down to the diffraction limit of the telescope), a clear 360 degree discovery space, have demonstrated very high contrast capabilities, are easy to implement on high-contrast imaging instruments, and have already been extensively tested on the sky. Since 2005, we have been designing, developing and testing an implementation of the charge-2 vector vortex phase mask based on concentric sub-wavelength gratings, referred to as the Annular Groove Phase Mask (AGPM). Science-grade mid-infrared AGPMs were produced in 2012 for the first time, using plasma etching on synthetic diamond substrates. They have been validated on a coronagraphic test bench, showing broadband peak rejection up to 500: 1 in the L band, which translates into a raw contrast of about 6 x 10(-5) at 2 lambda/D. Three of them have now been installed on world-leading diffraction-limited infrared cameras, namely VLT/NACO, VLT/VISIR and LBT/LMIRCam. During the science verification observations with our L-band AGPM on NACO, we observed the beta Pictoris system and obtained unprecedented sensitivity limits to planetary companions down to the diffraction limit (0 : 1 0 0). More recently, we obtained new images of the HR 8799 system at L band during the AGPM first light on LMIRCam. After reviewing these first results obtained with mid-infrared AGPMs, we will discuss the short-and mid-term goals of the on-going VORTEX project, which aims to improve the performance of our vortex phase masks for future applications on second-generation high-contrast imager and on future extremely large telescopes (ELTs). In particular, we will briefly describe our current efforts to improve the manufacturing of mid-infrared AGPMs, to push their operation to shorter wavelengths, and to provide deeper starlight extinction by creating new designs for higher topological charge vortices. Within the VORTEX project, we also plan to develop new image processing techniques tailored to coronagraphic images, and to study some pre- and post-coronagraphic concepts adapted to the vortex coronagraph in order to reduce scattered starlight in the final images.
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| 8. |
- Absil, Oliver, et al.
(författare)
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Three years of harvest with the vector vortex coronagraph in the thermal infrared
- 2016
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Ingår i: Ground-Based and Airborne Instrumentation for Astronomy VI. - : SPIE - International Society for Optical Engineering. - 9781510601963 ; , s. 1-14
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Konferensbidrag (refereegranskat)abstract
- For several years, we have been developing vortex phase masks based on sub-wavelength gratings, known as Annular Groove Phase Masks. Etched onto diamond substrates, these AGPMs are currently designed to be used in the thermal infrared (ranging from 3 to 13 μm). Our AGPMs were first installed on VLT/NACO and VLT/VISIR in 2012, followed by LBT/LMIRCam in 2013 and Keck/NIRC2 in 2015. In this paper, we review the development, commissioning, on-sky performance, and early scientific results of these new coronagraphic modes and report on the lessons learned. We conclude with perspectives for future developments and applications.
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| 9. |
- Alves, Rita, et al.
(författare)
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GATA2 at the mitosis-to-G1 transition is critical for definitive hematopoiesis
- 2021
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Ingår i: Experimental Hematology. - : Elsevier BV. - 1873-2399 .- 0301-472X. ; 100:Suppl, s. 35-35
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Konferensbidrag (refereegranskat)abstract
- In mitosis, transcription factors (TFs) and RNA polymerase disperse across the cytoplasm leading to transcriptional silencing, but some TFs are retained on condensed chromatin and mark genomic sites, a mechanism termed mitotic bookmarking. In pluripotent and differentiated cells this mechanism is important for pluripotency maintenance, cell reprogramming and lineage inheritance. However, the role of bookmarking in adult stem cells or in an in vivo system is yet to be addressed. Hematopoietic stem cells undergo drastic changes in cell cycle during development while balancing self-renewal and differentiation, suggesting a possible role for bookmarking.Here, we first addressed the mitotic retention capacity of the hemogenic TFs GATA2, GFI1B and FOS. We show that GATA2 remains bound to chromatin at all phases of cell cycle, as opposed to GFI1B and FOS. The C-terminal zinc finger (C-ZF) and the nuclear localization signal domains are required for GATA2 mitotic binding. Point mutations in the C-ZF associated with leukemia also impact GATA2 retention. To address the role of GATA2-mediated mitotic bookmarking, we have fused GATA2 to a mitosis degradation (MD) domain, which promotes protein destruction at the mitosis-to-G1 transition (M-G1). Degradation of GATA2 at M-G1 impacts the reprogramming of human fibroblasts to hemogenic cells. To address the role of GATA2 at M-G1 in vivo, we have generated a mouse model with the MD domain inserted upstream the Gata2 gene. Remarkably, homozygous mice are lethal, phenocopying Gata2 null mice which die at the onset of definitive hematopoiesis, showing a deficit in hematopoietic stem and progenitor cells.These findings implicate GATA2 as a mitotic bookmarking factor and its critical role at M-G1 for definitive hematopoiesis. Overall, our study highlights a dependency on mitotic bookmarkers for in vivo lineage commitment.
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| 10. |
- Aparicio, Francisco, et al.
(författare)
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Incorporation of luminescent nanometric films in photonic crystals and devices for the development of photonic sensors
- 2010
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Konferensbidrag (refereegranskat)abstract
- Dye molecules embedded in different matrices in the form of thin films are the basis of specific materials used for laser cavities, optical filters, optical gas sensors, etc. In the present communication we discuss a new methodology based on the remote microwave plasma assisted deposition of dye containing thin films that circumvent the above mentioned problems. It permits a tailored synthesis of optically active nanometric thin films containing dye molecules which are active as fluorescence emitters (i.e., coloured and fluorescent films). The principle of this new procedure is the partial polymerization of dye molecules that are evaporated over a substrate while exposed to a remote microwave Ar plasma. As a result of this process a polymeric thin film is produced in one step where some dye molecules keep intact their optical activity (although eventually, their optical response can be slightly modified by matrix effects). This methodology has been recently used for the deposition of novel plasma nanocomposites containing non-aggregated laser dyes to maximize the fluorescent emission of the materials and for the fabrication of optical NO2 sensing nanocomposites. To illustrate the possibilities of the technique we present here results for different fluorescent dye molecules, as perylene dyes, and several xanthene and oxazine derivative cationic dyes which are typically used as gain media in tuneable laser dyes. The luminescent, optical and sensing properties of these dye containing nanocomposites will be presented. These active optical layers are being developed for the fabrication of photonic sensor devices, optical filters and photonic chips (PHODYE EU Project). This is due to the full compatibility of the synthetic methodology with the present integrated microelectronic and optoelectronic technology. The possibilities for the fabrication of photonic devices integrating these active optical layers will be demonstrated. Especial attention will be paid to recent results about the incorporation of the luminescent films in photonic crystals and about the conformal growth of luminescent planar defects within artificial opals.
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