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2. Deep Learning architectures for generalized immunofluorescence based nuclear image segmentation

Author

Kromp, Florian, Fischer, Lukas, Bozsaky, Eva, Ambros, Inge, Doerr, Wolfgang, Taschner-Mandl, Sabine, Ambros, Peter, and Hanbury, Allan

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning, Quantitative Biology - Tissues and Organs
Abstract

Separating and labeling each instance of a nucleus (instance-aware segmentation) is the key challenge in segmenting single cell nuclei on fluorescence microscopy images. Deep Neural Networks can learn the implicit transformation of a nuclear image into a probability map indicating the class membership of each pixel (nucleus or background), but the use of post-processing steps to turn the probability map into a labeled object mask is error-prone. This especially accounts for nuclear images of tissue sections and nuclear images across varying tissue preparations. In this work, we aim to evaluate the performance of state-of-the-art deep learning architectures to segment nuclei in fluorescence images of various tissue origins and sample preparation types without post-processing. We compare architectures that operate on pixel to pixel translation and an architecture that operates on object detection and subsequent locally applied segmentation. In addition, we propose a novel strategy to create artificial images to extend the training set. We evaluate the influence of ground truth annotation quality, image scale and segmentation complexity on segmentation performance. Results show that three out of four deep learning architectures (U-Net, U-Net with ResNet34 backbone, Mask R-CNN) can segment fluorescent nuclear images on most of the sample preparation types and tissue origins with satisfactory segmentation performance. Mask R-CNN, an architecture designed to address instance aware segmentation tasks, outperforms other architectures. Equal nuclear mean size, consistent nuclear annotations and the use of artificially generated images result in overall acceptable precision and recall across different tissues and sample preparation types., Comment: 10 pages + 3 supplementary pages

Published
2019

4. A Protocol for Electron Probe Microanalysis (EPMA) of Monazite for Chemical Th-U-Pb Age Dating.

Author

Schulz, Bernhard, Krause, Joachim, and Dörr, Wolfgang

Subjects
ELECTRON probe microanalysis, ELECTRONIC probes, MONAZITE, ISOTOPIC analysis, PALEOZOIC Era
Abstract

A protocol for the monazite (LREE,Y,Th,U,Si,Ca)PO4 in situ Th-U-Pb dating by electron probe microanalyser (EPMA) involves a suitable reference monazite. Ages of several potential reference monazites were determined by TIMS-U-Pb isotope analysis. The EPMA protocol is based on calibration with REE-orthophosphates and a homogeneous Th-rich reference monazite at beam conditions of 20 kV, 50 nA, and 5 µm for best possible matrix matches and avoidance of dead time bias. EPMA measurement of samples and repeated analysis of the reference monazite are performed at beam conditions of 20 kV, 100 nA, and 5 µm. Analysis of Pb and U on a PETL crystal requires YLg-on-PbMa and ThMz-on-UMb interference corrections. Offline re-calibration of the Th calibration on the Th-rich reference monazite, to match its nominal age, is an essential part of the protocol. EPMA-Th-U-Pb data are checked in ThO2*-PbO coordinates for matching isochrones along regressions forced through zero. Error calculations of monazite age populations are performed by weighted average routines. Depending on the number of analyses and spread in ThO2*-PbO coordinates, minimum errors <10 Ma are possible and realistic for Paleozoic monazite ages. A test of the protocol was performed on two garnet metapelite samples from the Paleozoic metamorphic Zone of Erbendorf-Vohenstrauß (NE-Bavaria, western Bohemian Massif). [ABSTRACT FROM AUTHOR]

Published
2024
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5. Sonstige Therapieformen – Hämotherapie – Ernährung – apparativ – onkologisch – alternativ – perspektivisch

Author

Thiele, Thomas, Selleng, Kathleen, Ranft, Andreas, Kochs, Eberhard Friedrich, Waldfahrer, Frank, Leuwer, Rudolf, Klein, Martin, Appold, Steffen, Folprecht, Gunnar, Schuler, Patrick, Dörr, Wolfgang, Dörr, Elke, Grötz, Knut A., Riesenbeck, Dorothea, Friese, Karl-Heinz, Plath, Michaela, Zaoui, Karim, and Reiß, Michael, editor

Published
2021
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8. Provenance of lower Palaeozoic metasediments of the East Odenwald (Mid-German-Crystalline Zone, Variscides) — a correlation with the East European Platform (Poland)

Author

Dörr, Wolfgang, Stein, Eckhardt, Kirchner, Ferdinand, Meinaß, Henri Paul, Velledits, Felicitás, Dörr, Wolfgang, Stein, Eckhardt, Kirchner, Ferdinand, Meinaß, Henri Paul, and Velledits, Felicitás

Abstract

U–Pb age spectra of detrital zircons related to the East European Platform could be traced in paragneiss through the whole Mid-German-Crystalline Zone (Variscides, Central Europe) from the Odenwald via the Spessart to the Ruhla crystalline forming an exotic unit between Armorica and Laurussia. The depositional ages of the paragneiss are defined by the youngest age of the detrital zircons and the oldest intrusion ages as Ordovician to Silurian. The Ediacaran dominated age spectrum of detrital zircons from the paragneiss of the East Odenwald suggests the latter to be derived from the shelf of the East European Platform (Baltica), which was influenced by the 1.5 Ga old detritus delivered from a giant intrusion (Mazury granitoid, Poland). The detrital zircon age spectrum of the lower Palaeozoic paragneiss of the East Odenwald and sandstone of the northern Holy Cross Mountains are identical. The pure Sveconorwegian spectrum of the lower Palaeozoic quartzite from the Spessart, (Kirchner and Albert Int J Earth Sci 2020) and the Ruhla (Zeh and Gerdes Gondwana Res 17:254–263, 2010) could be sourced from Bornholm and southern Sweden. A U–Pb age spectrum with 88% Palaeozoic detrital zircons from a volcano-sedimentary rock of the East Odenwald is interpreted to be derived from a Silurian magmatic arc (46%), which was probably generated during the drift of the Mid-German-Crystalline Zone micro-continent to the south. A tentative plate tectonic model of Mid-German-Crystalline Zone is presented taking into account (a) the East European Platform related age spectra of the detrital zircons (b) the Ordovician to Silurian depositional age of the metasediments (c) the Silurian and Early Devonian intrusion age of the plutonic and volcanic rocks and (d) the U–Pb ages of the Middle Devonian high-grade metamorphism. The East European Platform-related part of the Mid-German-Crystalline Zone is interpreted as a micro-continent, which drifted through the Rheic Ocean to the south and collided

Published
2024

27. Dose–volume effect relationships for late rectal morbidity in patients treated with chemoradiation and MRI-guided adaptive brachytherapy for locally advanced cervical cancer: Results from the prospective multicenter EMBRACE study

Author

Mazeron, Renaud, Fokdal, Lars U., Kirchheiner, Kathrin, Georg, Petra, Jastaniyah, Noha, Šegedin, Barbara, Mahantshetty, Umesh, Hoskin, Peter, Jürgenliemk-Schulz, Ina, Kirisits, Christian, Lindegaard, Jacob C., Dörr, Wolfgang, Haie-Meder, Christine, Tanderup, Kari, and Pötter, Richard

Published
2016
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28. Effect of tumor dose, volume and overall treatment time on local control after radiochemotherapy including MRI guided brachytherapy of locally advanced cervical cancer

Author

Tanderup, Kari, Fokdal, Lars Ulrik, Sturdza, Alina, Haie-Meder, Christine, Mazeron, Renaud, van Limbergen, Erik, Jürgenliemk-Schulz, Ina, Petric, Primoz, Hoskin, Peter, Dörr, Wolfgang, Bentzen, Søren M., Kirisits, Christian, Lindegaard, Jacob Christian, and Pötter, Richard

Published
2016
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29. Health-Related Quality of Life in Locally Advanced Cervical Cancer Patients After Definitive Chemoradiation Therapy Including Image Guided Adaptive Brachytherapy: An Analysis From the EMBRACE Study

Author

Lindegaard, Jacob, Tanderup, Kari, Fokdal, Lars, Van Der Steen Banasik, Elzbieta, Haie-Meder, Christine, Dumas, Isabelle, Chargari, Cyrus, Nout, Remi A., Van Limbergen, Erik, Petrič, Primož, Segedin, Barbara, Hudej, Robert, Erickson, Beth, Hoskin, Peter, Lowe, Gerry, Mahantshetty, Umesh, Swamidas, Jamema, Shrivastava, Shyam Kishore, Jürgenliemk-Schulz, Ina M., De Leeuw, Astrid, Kirchheiner, Kathrin, Dörr, Wolfgang, Pötter, Richard, Lutgens, Ludy C.H.W., Hadjiev, Janaki, Cooper, Rachel, Bownes, Peter, Sundset, Marit, Bruheim, Kjersti, Hellebust, Taran Paulsen, Huang, Fleur, Menon, Geetha, Villafranca, Elena, Rai, Bhavana, Oinam, Arun S., Tan, Li Tee, Bachand, Francois, Jacobson, Geraldine, Anttila, Maarit, Pieters, Bradley, and Lindegaard, Jacob C.

Published
2016
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39. THE DOSE AND DOSE-RATE EFFECTIVENESS FACTOR (DDREF)

Author

Wakeford, Richard, Azizova, Tamara, Dörr, Wolfgang, Garnier-Laplace, Jacqueline, Hauptmann, Michael, Ozasa, Kotaro, Rajaraman, Preetha, Sakai, Kazuo, Salomaa, Sisko, Sokolnikov, Mikhail, Stram, Dan, Sun, Quanfu, Wojcik, Andrzej, Woloschak, Gayle, Bouffler, Simon, Grosche, Bernd, Kai, Michiaki, Little, Mark P., Shore, Roy E., Walsh, Linda, and Rühm, Werner

Published
2019
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46. Pre-Variscan (Lower Devonian) deformation of the Silurian magmatic arc of the East Odenwald (Mid-German Crystalline Zone, Variscides)

Author

Meinaß , Henri Paul, Dörr , Wolfgang, and Stein , Eckardt

Subjects
General Earth and Planetary Sciences
Abstract

The Böllstein Odenwald is forming a large anticline of mainly pre-Devonian rock in the Mid-German Crystalline Zone (MCGZ). The contact between core and schist envelope of the anticline is well exposed at Weichberg quarry. Metasedimentary rocks of the schist envelope are intruded by granodioritic sills of a Silurian magmatic arc, showing at least two folding phases: Recumbent tight isoclinal folds are overprinted by upright gentle folds. A pegmatite dike, intruding at 411 ±2 Ma (U-Pb analyses on zircon) into the schist envelope rocks, crosscuts perpendicular to the main foliation. It shows only a weak schistosity related to the isoclinal folding, which therefore must have been active in Lower Devonian (>411 ±2 Ma; Lochkovian/Pragian) after the Silurian intrusion of the granodiorite sills (U-Pb on zircon ca. 423 Ma, Dörr et al. in press). The Lower Devonian deformation of the East Odenwald probably results from the collision of the MGCZ with the NW boundary of the Saxothuringian Zone. The core is represented by a (meta)granite intruding into the schist envelope at 404 ±2 Ma (U-Pb method on zircon). A deformed fold directly at the contact between metagranite and metasediments and dikes terminated at the contact point to eastward directed tectonic movements between core and schist envelope after 404 ±2 Ma, probably at 375 Ma (U-Pb on zircon, Todt et al. 1995). These results are compared to other units occupying a similar position in the European Variscides and help to clarify the position of the East Odenwald during Variscan orogeny.

Published
2022

50. Epac contributes to cardiac hypertrophy and amyloidosis induced by radiotherapy but not fibrosis

Author

Monceau, Virginie, Llach, Anna, Azria, David, Bridier, André, Petit, Benoît, Mazevet, Marianne, Strup-Perrot, Carine, To, Thi-Hong-Van, Calmels, Lucie, Germaini, Marie-Michèle, Gourgou, Sophie, Fenoglietto, Pascal, Bourgier, Céline, Gomez, Ana-Maria, Escoubet, Brigitte, Dörr, Wolfgang, Haagen, Julia, Deutsch, Eric, Morel, Eric, and Vozenin, Marie Catherine

Published
2014
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