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  • 11
    In: BMC Bioinformatics, Springer Science and Business Media LLC, Vol. 23, No. 1 ( 2022-07-21)
    Abstract: The segmentation of 3D cell nuclei is essential in many tasks, such as targeted molecular radiotherapies (MRT) for metastatic tumours, toxicity screening, and the observation of proliferating cells. In recent years, one popular method for automatic segmentation of nuclei has been deep learning enhanced marker-controlled watershed transform. In this method, convolutional neural networks (CNNs) have been used to create nuclei masks and markers, and the watershed algorithm for the instance segmentation. We studied whether this method could be improved for the segmentation of densely cultivated 3D nuclei via developing multiple system configurations in which we studied the effect of edge emphasizing CNNs, and optimized H-minima transform for mask and marker generation, respectively. Results The dataset used for training and evaluation consisted of twelve in vitro cultivated densely packed 3D human carcinoma cell spheroids imaged using a confocal microscope. With this dataset, the evaluation was performed using a cross-validation scheme. In addition, four independent datasets were used for evaluation. The datasets were resampled near isotropic for our experiments. The baseline deep learning enhanced marker-controlled watershed obtained an average of 0.69 Panoptic Quality (PQ) and 0.66 Aggregated Jaccard Index (AJI) over the twelve spheroids. Using a system configuration, which was otherwise the same but used 3D-based edge emphasizing CNNs and optimized H-minima transform, the scores increased to 0.76 and 0.77, respectively. When using the independent datasets for evaluation, the best performing system configuration was shown to outperform or equal the baseline and a set of well-known cell segmentation approaches. Conclusions The use of edge emphasizing U-Nets and optimized H-minima transform can improve the marker-controlled watershed transform for segmentation of densely cultivated 3D cell nuclei. A novel dataset of twelve spheroids was introduced to the public.
    Type of Medium: Online Resource
    ISSN: 1471-2105
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
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  • 12
    In: European Radiology Experimental, Springer Science and Business Media LLC, Vol. 7, No. 1 ( 2023-06-21)
    Abstract: Early diagnosis of the potentially fatal but curable chronic pulmonary embolism (CPE) is challenging. We have developed and investigated a novel convolutional neural network (CNN) model to recognise CPE from CT pulmonary angiograms (CTPA) based on the general vascular morphology in two-dimensional (2D) maximum intensity projection images. Methods A CNN model was trained on a curated subset of a public pulmonary embolism CT dataset (RSPECT) with 755 CTPA studies, including patient-level labels of CPE, acute pulmonary embolism (APE), or no pulmonary embolism. CPE patients with right-to-left-ventricular ratio (RV/LV)  〈  1 and APE patients with RV/LV  ≥ 1 were excluded from the training. Additional CNN model selection and testing were done on local data with 78 patients without the RV/LV-based exclusion. We calculated area under the receiver operating characteristic curves (AUC) and balanced accuracies to evaluate the CNN performance. Results We achieved a very high CPE versus no-CPE classification AUC 0.94 and balanced accuracy 0.89 on the local dataset using an ensemble model and considering CPE to be present in either one or both lungs. Conclusions We propose a novel CNN model with excellent predictive accuracy to differentiate chronic pulmonary embolism with RV/LV  ≥ 1 from acute pulmonary embolism and non-embolic cases from 2D maximum intensity projection reconstructions of CTPA. Relevance statement A DL CNN model identifies chronic pulmonary embolism from CTA with an excellent predictive accuracy. Key points • Automatic recognition of CPE from computed tomography pulmonary angiography was developed. • Deep learning was applied on two-dimensional maximum intensity projection images. • A large public dataset was used for training the deep learning model. • The proposed model showed an excellent predictive accuracy. Graphical Abstract
    Type of Medium: Online Resource
    ISSN: 2509-9280
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 2905812-0
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  • 13
    In: Physical Review D, American Physical Society (APS), Vol. 103, No. 10 ( 2021-5-20)
    Type of Medium: Online Resource
    ISSN: 2470-0010 , 2470-0029
    Language: English
    Publisher: American Physical Society (APS)
    Publication Date: 2021
    detail.hit.zdb_id: 2844732-3
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  • 14
    In: Journal of Geophysical Research: Solid Earth, American Geophysical Union (AGU), Vol. 128, No. 3 ( 2023-03)
    Abstract: Baseline vectors between legacy antennas and co‐located VGOS antennas are obtained from phase delays with the highest possible precision Sources of error in short‐baseline observations are investigated at the 1 mm level in terms of their potential impacts
    Type of Medium: Online Resource
    ISSN: 2169-9313 , 2169-9356
    Language: English
    Publisher: American Geophysical Union (AGU)
    Publication Date: 2023
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    detail.hit.zdb_id: 3094197-0
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  • 15
    In: Experimental Astronomy, Springer Science and Business Media LLC, Vol. 51, No. 3 ( 2021-06), p. 559-594
    Abstract: This paper presents the ESA Voyage 2050 White Paper for a concept of TeraHertz Exploration and Zooming-in for Astrophysics (THEZA). It addresses the science case and some implementation issues of a space-borne radio interferometric system for ultra-sharp imaging of celestial radio sources at the level of angular resolution down to (sub-) microarcseconds. THEZA focuses at millimetre and sub-millimetre wavelengths (frequencies above $\sim $ ∼ 300 GHz), but allows for science operations at longer wavelengths too. The THEZA concept science rationale is focused on the physics of spacetime in the vicinity of supermassive black holes as the leading science driver. The main aim of the concept is to facilitate a major leap by providing researchers with orders of magnitude improvements in the resolution and dynamic range in direct imaging studies of the most exotic objects in the Universe, black holes. The concept will open up a sizeable range of hitherto unreachable parameters of observational astrophysics. It unifies two major lines of development of space-borne radio astronomy of the past decades: Space VLBI (Very Long Baseline Interferometry) and mm- and sub-mm astrophysical studies with “single dish” instruments. It also builds upon the recent success of the Earth-based Event Horizon Telescope (EHT) – the first-ever direct image of a shadow of the super-massive black hole in the centre of the galaxy M87. As an amalgam of these three major areas of modern observational astrophysics, THEZA aims at facilitating a breakthrough in high-resolution high image quality studies in the millimetre and sub-millimetre domain of the electromagnetic spectrum.
    Type of Medium: Online Resource
    ISSN: 0922-6435 , 1572-9508
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
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  • 16
    In: Nature, Springer Science and Business Media LLC, Vol. 616, No. 7958 ( 2023-04-27), p. 686-690
    Abstract: The nearby radio galaxy M87 is a prime target for studying black hole accretion and jet formation 1,2 . Event Horizon Telescope observations of M87 in 2017, at a wavelength of 1.3 mm, revealed a ring-like structure, which was interpreted as gravitationally lensed emission around a central black hole 3 . Here we report images of M87 obtained in 2018, at a wavelength of 3.5 mm, showing that the compact radio core is spatially resolved. High-resolution imaging shows a ring-like structure of $${8.4}_{-1.1}^{+0.5}$$ 8.4 − 1.1 + 0.5 Schwarzschild radii in diameter, approximately 50% larger than that seen at 1.3 mm. The outer edge at 3.5 mm is also larger than that at 1.3 mm. This larger and thicker ring indicates a substantial contribution from the accretion flow with absorption effects, in addition to the gravitationally lensed ring-like emission. The images show that the edge-brightened jet connects to the accretion flow of the black hole. Close to the black hole, the emission profile of the jet-launching region is wider than the expected profile of a black-hole-driven jet, suggesting the possible presence of a wind associated with the accretion flow.
    Type of Medium: Online Resource
    ISSN: 0028-0836 , 1476-4687
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    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
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  • 17
    In: Acta Astronautica, Elsevier BV, Vol. 196 ( 2022-07), p. 314-333
    Type of Medium: Online Resource
    ISSN: 0094-5765
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2022
    detail.hit.zdb_id: 2014614-0
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  • 18
    Online Resource
    Online Resource
    Cambridge University Press (CUP) ; 2010
    In:  Proceedings of the International Astronomical Union Vol. 6, No. S275 ( 2010-09), p. 275-279
    In: Proceedings of the International Astronomical Union, Cambridge University Press (CUP), Vol. 6, No. S275 ( 2010-09), p. 275-279
    Abstract: A model for OJ 287 consisting of two orbiting black holes has been constructed using optical light curve data. The model has successfully predicted the occurrence of sharp optical outbursts of OJ 287 for the past 15 years. Here we test if also the variations in the radio jet position angle can be explained within the framework of this same model, which has most of its parameters fixed by the timing of the optical flares. The model applied here has only three free parameters left, the (trivial) zero point of the jet position angle, the time lag between changes in the disk and jet orientations, and the zero point of the viewing angle. Despite its simplicity and the small number of free parameters, the model appears to be able to reproduce the main properties of the observed position angle variations during the past 30 years. The best fits are obtained when the time lag is either ~4 or ~14 years. However, the jet orientation seems to be unrelated to the direction of the spin of the primary black hole. This implies, assuming that the basic model is correct, that the mean orientation of the jet is determined by the orientation of the inner accretion disk, not by the spin axis of the black hole.
    Type of Medium: Online Resource
    ISSN: 1743-9213 , 1743-9221
    Language: English
    Publisher: Cambridge University Press (CUP)
    Publication Date: 2010
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  • 19
    In: Astronomy & Astrophysics, EDP Sciences, Vol. 672 ( 2023-04), p. A130-
    Abstract: Measuring and inferring the key physical parameters of jets in active galactic nuclei (AGN) requires high-resolution very long baseline interferometry (VLBI) observations. Using VLBI to measure a core-shift effect is a common way of obtaining estimates of the jet magnetic field strength, a key parameter for understanding jet physics. The VLBI core is typically identified as the bright feature at the upstream end of the jet, and the position of this feature changes with the observed frequency, r core  ∝  ν −1/ k r . Due to the variable nature of AGN, flares can cause variability of the measured core shift. In this work, we investigated the time variability of the core-shift effect in the luminous blazar 3C 454.3 . We employed a self-referencing analysis of multi-frequency (5, 8, 15, 22−24, and 43 GHz) Very Long Baseline Array (VLBA) data covering 19 epochs from 2005 to 2010. We found significant core-shift variability ranging from 0.27 to 0.86 milliarcsec between 5 GHz and 43 GHz. These results confirm the core-shift variability phenomenon observed previously. Furthermore, we also found time variability of the core-shift index, k r , which was typically below one, with an average value of 0.85 ± 0.08 and a standard deviation of 0.30. Values of k r below one were found during flaring and quiescent states. Our results indicate that the commonly assumed conical jet shape and equipartition conditions do not always hold simultaneously. Even so, these conditions are typically assumed when deriving magnetic field strengths from core-shift measurements, which can lead to unreliable results if k r significantly deviates from unity. Therefore, it is necessary to verify that k r  = 1 actually holds before using core-shift measurements and the equipartition assumption to derive physical conditions in the jets. When k r  = 1 epochs are selected in the case of 3C 454.3 , the magnetic field estimates are consistent, even though the core shift varies significantly with time. Subsequently, we estimated the magnetic flux in the jet of 3C 454.3 and found that the source is in the magnetically arrested disc state, which agrees with earlier studies. Finally, we found a good correlation of the core position with the core flux density, r core  ∝  S core 0.7 , which is consistent with increased particle density during the flares.
    Type of Medium: Online Resource
    ISSN: 0004-6361 , 1432-0746
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    Language: English
    Publisher: EDP Sciences
    Publication Date: 2023
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    SSG: 16,12
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  • 20
    In: Rheumatology International, Springer Science and Business Media LLC, Vol. 42, No. 6 ( 2022-06), p. 1015-1025
    Abstract: Considerable proportion of patients with SpA have been immunized to the subcutaneous anti-TNF drug they are using. Concomitant use of MTX protects from immunization, whereas SASP does not. Patients with SpA using subcutaneous anti-TNF drugs can benefit from monitoring of the drug trough levels. Abstract Immunization to biological drugs can lead to decreased efficacy and increased risk of adverse effects. The objective of this cross-sectional study was to assess the extent and significance of immunization to subcutaneous tumor necrosis factor (TNF) inhibitors in axial spondyloarthritis (axSpA) patients in real-life setting. A serum sample was taken 1–2 days before the next drug injection. Drug trough concentrations, anti-drug antibodies (ADAb) and TNF-blocking capacity were measured in 273 patients with axSpA using subcutaneous anti-TNF drugs. The clinical activity of SpA was assessed using the Bath AS Disease Activity Index (BASDAI) and the Maastricht AS Entheses Score (MASES). ADAb were found in 11% of the 273 patients: in 21/99 (21%) of patients who used adalimumab, in 0/83 (0%) of those who used etanercept, in 2/79 (3%) of those who used golimumab and in 6/12 (50%) of those who used certolizumab pegol. Use of methotrexate reduced the risk of formation of ADAb, whereas sulfasalazine did not. Presence of ADAb resulted in decreased drug concentration and reduced TNF-blocking capacity. However, low levels of ADAb had no effect on TNF-blocking capacity and did not correlate with disease activity. The drug trough levels were below the consensus target level in 36% of the patients. High BMI correlated with low drug trough concentration. Patients with low drug trough levels had higher disease activity. The presence of anti-drug antibodies was associated with reduced drug trough levels, and the patients with low drug trough levels had higher disease activity. The drug trough levels were below target level in significant proportion of patients and, thus, measuring the drug concentration and ADAb could help to optimize the treatment in SpA patients.
    Type of Medium: Online Resource
    ISSN: 1437-160X
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 1464208-6
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