Despite significant advancements in three-dimensional (3D) cell culture technology and the acquisition of extensive data, there is an ongoing need for more effective and dependable data analysis methods. These concerns arise from the continued reliance on manual quantification techniques. In this study, we introduce a microphysiological system (MPS) that seamlessly integrates 3D cell culture to acquire large-scale imaging data and employs deep learning-based virtual staining for quantitative angiogenesis analysis. We utilize a standardized microfluidic device to obtain comprehensive angiogenesis data. Introducing Angio-Net, a novel solution that replaces conventional immunocytochemistry, we convert brightfield images into label-free virtual fluorescence images through the fusion of SegNet and cGAN. Moreover, we develop a tool capable of extracting morphological blood vessel features and automating their measurement, facilitating precise quantitative analysis. This integrated system proves to be invaluable for evaluating drug efficacy, including the assessment of anticancer drugs on targets such as the tumor microenvironment. Additionally, its unique ability to enable live cell imaging without the need for cell fixation promises to broaden the horizons of pharmaceutical and biological research. Our study pioneers a powerful approach to high-throughput angiogenesis analysis, marking a significant advancement in MPS.
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Variant calling using long-read RNA sequencing (lrRNA-seq) can be applied to diverse tasks, such as capturing full-length isoforms and gene expression profiling. It poses challenges, however, due to higher error rates than DNA data, the complexities of transcript diversity, RNA editing events, etc. In this paper, we propose Clair3-RNA, the first deep learning-based variant caller tailored for lrRNA-seq data.
View Article and Find Full Text PDFAlphaFold2 (AF2), a deep-learning based model that predicts protein structures from their amino acid sequences, has recently been used to predict multiple protein conformations. In some cases, AF2 has successfully predicted both dominant and alternative conformations of fold-switching proteins, which remodel their secondary and tertiary structures in response to cellular stimuli. Whether AF2 has learned enough protein folding principles to reliably predict alternative conformations outside of its training set is unclear.
View Article and Find Full Text PDFPhys Imaging Radiat Oncol
October 2024
Université Paris-Saclay, Gustave Roussy, Inserm, Molecular Radiotherapy and Therapeutic Innovation, U1030, 94800 Villejuif, France.
Background And Purpose: Deep-learning-based automatic segmentation is widely used in radiation oncology to delineate organs-at-risk. Dual-energy CT (DECT) allows the reconstruction of enhanced contrast images that could help with manual and auto-delineation. This paper presents a performance evaluation of a commercial auto-segmentation software on image series generated by a DECT.
View Article and Find Full Text PDFHealth Inf Sci Syst
December 2025
Faculty of Information Engineering and Automation, Kunming University of Science and Technology, No.727 Jingming South Road, Kunming, 650504 Yunnan China.
For diagnosing mental health conditions and assessing sleep quality, the classification of sleep stages is essential. Although deep learning-based methods are effective in this field, they often fail to capture sufficient features or adequately synthesize information from various sources. For the purpose of improving the accuracy of sleep stage classification, our methodology includes extracting a diverse array of features from polysomnography signals, along with their transformed graph and time-frequency representations.
View Article and Find Full Text PDFHeliyon
January 2025
John von Neumann Faculty of Informatics, Obuda University, Budapest, Hungary.
Global adoption of wind energy continues to increase, while improving the efficiency of turbine settings requires reliable wind speed (WS) models. The latest models rely on artificial intelligence (AI) optimizations which constructs tests on a range of novel hybrid models to examine the reliability. Gradient Boosting (GB), Random Forest (RF), and Long Short-Term Memory (LSTM) are used in new combinations for data pre-processing.
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