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Improving 3D deep learning segmentation with biophysically motivated cell synthesis.
Commun Biol
January 2025
Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany.
Biomedical research increasingly relies on three-dimensional (3D) cell culture models and artificial-intelligence-based analysis can potentially facilitate a detailed and accurate feature extraction on a single-cell level. However, this requires for a precise segmentation of 3D cell datasets, which in turn demands high-quality ground truth for training. Manual annotation, the gold standard for ground truth data, is too time-consuming and thus not feasible for the generation of large 3D training datasets.
View Article and Find Full Text PDFA three-dimensional mouse liver organoid platform for assessing EDCs metabolites simulating liver metabolism.
Environ Int
January 2025
Department of Agricultural Biotechnology, Seoul National University, Seoul 00826, Republic of Korea; Department of Food and Animal Biotechnology, Seoul National University, Seoul 00826, Republic of Korea; Center for Food and Bioconvergence, Research Institute for Agricultural and Life Sciences, Interdisciplinary Programs in Agricultural Genomics, Seoul National University, Seoul 00826, Republic of Korea; Green Bio Science & Technology, Bio-Food Industrialization, Seoul National University, 1447 Pyeongchang-daero, Daehwa-myeon, Pyeongchang-gun, Gangwon-do 25354, Republic of Korea. Electronic address:
Hepatic metabolism is an important process for evaluate the potential activity and toxicity of endocrine disrupting chemicals (EDCs) metabolites. Organization for Economic Co-operation and Development (OECD) has advocated the development of in vitro assays that mimic in vivo hepatic metabolism to eventually replace classical animal tests. In response to this need, we established a 3D mouse liver organoid (mLO) platform that mimics the animal model and is distinct from existing models.
View Article and Find Full Text PDFProtocol for the three-dimensional analysis of rodent skeletal muscle.
STAR Protoc
January 2025
Stem Cell Institute, University of Minnesota Medical School, Minneapolis, MN, USA; Paul & Sheila Wellstone Muscular Dystrophy Center, University of Minnesota Medical School, Minneapolis, MN, USA; Department of Neurology, University of Minnesota Medical School, Minneapolis, MN, USA. Electronic address:
Confocal imaging is a powerful tool capable of analyzing cellular spatial data within a given tissue. Here, we present a protocol for preparing optically cleared extensor digitorum longus (EDL) skeletal muscle samples suitable for confocal imaging/computational analysis. We describe steps for sample preparation (including perfusion fixation and tissue clearing of muscle samples), image acquisition, and computational analysis, with sample segmentation/3D rendering outlined.
View Article and Find Full Text PDFA Two-Step Protocol for Isolation and Maintenance of Lung Cancer Primary 3D Cultures.
Cancers (Basel)
December 2024
Translational Research Laboratory, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy.
Background/objectives: Despite the introduction of innovative therapeutics, lung cancer is still the leading cause of cancer-related death. For this reason, lung cancer still requires deep characterization to identify cellular and molecular targets that can be used to develop novel therapeutic strategies. Three-dimensional cellular models, including patient-derived organoids (PDOs), represent useful tools to study lung cancer biology and may be employed in the future as predictive tools in therapeutic decisions.
View Article and Find Full Text PDFS6K2 in Focus: Signaling Pathways, Post-Translational Modifications, and Computational Analysis.
Int J Mol Sci
December 2024
Division of Cancer, Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, London W12 0NN, UK.
S6 Kinase 2 (S6K2) is a key regulator of cellular signaling and is crucial for cell growth, proliferation, and survival. This review is divided into two parts: the first focuses on the complex network of upstream effectors, downstream modulators, and post-translational modifications (PTMs) that regulate S6K2 activity. We emphasize the dynamic nature of S6K2 regulation, highlighting its critical role in cellular homeostasis and its potential as a therapeutic target in diseases like cancer.
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