@article{21839,
  abstract     = {Background & Aims: To develop and validate a CT-based radiomics model to assess HVPG and predict a composite endpoint of liver-related events (LRE: decompensation and liver-related death) in patients with cirrhosis.

Methods: This retrospective study included 357 cirrhosis patients, who received invasive HVPG measurements, 120 liver-healthy controls (training cohort) and 85 and 100 cirrhosis patients (internal and external validation cohorts, respectively), and contrast-enhanced abdominal CTs. After volumetric segmentation of the liver and spleen on CT, Bayesian parameter optimization was used for selection of extracted features and hyperparameter tuning in random forest or elastic net models. Prediction accuracy was evaluated using Pearson correlation coefficients of predicted (’radio-HVPG’) and invasive HVPG. Discrimination between relevant HVPG cut-offs was determined by receiver operating characteristic (ROC) analysis. The predictive value of radio-HVPG and invasive-HVPG for LRE was compared using Cox regression models.

Results: Radio-HVPG, predicted by an optimized random forest model based on 74 selected CT features, correlated with invasive-HVPG and detected clinically significant portal hypertension (CSPH: HVPG ≥ 10 mmHg) on the internal (Pearson r = 0.63, AUC 0.89 [95% CI: 0.81–0.96]) and external (Pearson r = 0.62, AUC 0.80 [95% CI: 0.64–0.91]) validation cohorts. Radio-HVPG predicted LRE when adjusting for MELD and albumin (adjusted HR: 1.14 [95% CI: 1.04–1.25], p = 0.005) and performed similarly to invasive-HVPG.

Conclusions: Radiomic features accurately predict HVPG in patients with cirrhosis and allow risk stratification for LRE in a radiomics-clinical signature.},
  author       = {Sin, Celine and Watzenboeck, Martin Luther and Iofinova, Eugenia B and Balcar, Lorenz and Semmler, Georg and Scheiner, Bernhard and Lampichler, Katharina and Mandorfer, Mattias and Moga, Lucile and Rautou, Pierre‐Emmanuel and Ronot, Maxime and Menche, Jörg and Reiberger, Thomas and Scharitzer, Martina},
  issn         = {1478-3231},
  journal      = {Liver International},
  keywords     = {computed tomography, liver, portal hypertension, radiomics, spleen},
  number       = {5},
  publisher    = {Wiley},
  title        = {{Radiomics‐based assessment of portal hypertension severity and risk stratification of cirrhotic patients using routine CT scans}},
  doi          = {10.1111/liv.70633},
  volume       = {46},
  year         = {2026},
}

@article{21572,
  abstract     = {This study focuses on advancing metascintillators to break the 100 ps barrier and approach the 10 ps target. We exploitnanophotonic features, specifically the Purcell effect, to shape and enhance the scintillation properties of the first-generation metascintillator. We demonstrate that a faster emission is achievable along with a more efficient conversionefficiency. This results in a coincidence time resolution improved by a factor of 1.3, crucial for TOF-PET applications.},
  author       = {Shultzman, A. and Schütz, R. and Kurman, Y. and Lahav, N. and Dosovitskiy, G. and Roques-Carmes, Charles and Bekenstein, Y. and Konstantinou, G. and Latella, R. and Zhang, L. and Loignon-Houle, F. and Gonzalez, A. J. and Benlloch, J. M. and Kaminer, I. and Lecoq, P.},
  issn         = {2469-7303},
  journal      = {IEEE Transactions on Radiation and Plasma Medical Sciences},
  keywords     = {Nanophotonics, Positron emission tomography, scintillators},
  number       = {2},
  pages        = {141--147},
  publisher    = {Institute of Electrical and Electronics Engineers},
  title        = {{Toward a second generation of metascintillators using the Purcell effect}},
  doi          = {10.1109/trpms.2024.3471251},
  volume       = {9},
  year         = {2025},
}

@misc{14502,
  abstract     = {A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized fila- mentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner.},
  author       = {Dimchev, Georgi A and Amiri, Behnam and Fäßler, Florian and Falcke, Martin and Schur, Florian KM},
  keywords     = {cryo-electron tomography, actin cytoskeleton, toolbox},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data}},
  doi          = {10.15479/AT:ISTA:14502},
  year         = {2023},
}

@phdthesis{12491,
  abstract     = {The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. 
Despite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. 
In this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). 
To this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. 
In order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. 
High-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. 
In summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions.},
  author       = {Zens, Bettina},
  isbn         = {978-3-99078-027-5},
  issn         = {2663-337X},
  keywords     = {cryo-EM, cryo-ET, FIB milling, method development, FIBSEM, extracellular matrix, ECM, cell-derived matrices, CDMs, cell culture, high pressure freezing, HPF, structural biology, tomography, collagen},
  pages        = {187},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography}},
  doi          = {10.15479/at:ista:12491},
  year         = {2023},
}

@misc{5557,
  abstract     = {Small synthetic discrete tomography problems.
Sizes are 32x32, 64z64 and 256x256.
Projection angles are 2, 4, and 6.
Number of labels are 3 and 5.},
  author       = {Swoboda, Paul},
  keywords     = {discrete tomography},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Synthetic discrete tomography problems}},
  doi          = {10.15479/AT:ISTA:46},
  year         = {2016},
}