Computational analysis of cell dynamic morphology in time-lapse image is a challenging task in biomedical research. Inspired by the recent success of deep learning, we investigate the possibility to apply a deep neural network to cell dynamic morphology analysis in this paper. Specifically, a contour spectrum is composed as the input of neural network to characterize cell spatiotemporal deformation, then a pre-trained convolutional neural network model is performed for automatic feature extraction. Finally, the extracted deep convolutional features are analyzed by SVM. Experimental results demonstrate that the proposed strategy outperforms existing methods on the live-cell database, and the features extracted by the last layer and classified by linear kernel SVM allows for the state-of-the-art performance.
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http://dx.doi.org/10.1109/EMBC.2017.8037414 | DOI Listing |
Biophys J
January 2025
Department of Physics and Astronomy, Department of Chemistry, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California, USA. Electronic address:
In this work we present a minimal structure-based model of protein diffusional search along local DNA amid protein binding and unbinding events on the DNA, taking into account protein-DNA electrostatic interactions and hydrogen-bonding (HB) interactions or contacts at the interface. We accordingly constructed the protein diffusion-association/dissociation free energy surface and mapped it to 1D as the protein slides along DNA, maintaining the protein-DNA interfacial HB contacts that presumably dictate the DNA sequence information detection. Upon DNA helical path correction, the protein 1D diffusion rates along local DNA can be physically derived to be consistent with experimental measurements.
View Article and Find Full Text PDFUltrasound Med Biol
January 2025
Institute of Biomedical Technologies, Auckland University of Technology, Auckland City, 1010, Auckland, New Zealand. Electronic address:
Objective: This study aims to evaluate the viability of a hypothesis for selective targeting of skin cancer cells by exploiting the spectral gap with healthy cells using analytical and numerical simulation.
Methods: The spectral gap was first identified using a viscoelastic dynamic model, with the physical and mechanical properties of healthy and cancerous skin cells deduced from previous experimental studies conducted on cell lines. The outcome of the analytical simulation was verified numerically using modal and harmonic analysis.
J Dermatol Sci
December 2024
Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan; Department of Dermatology, Tohoku University Graduate School of Medicine, Sendai, Japan. Electronic address:
Background: Altered Fli1 expression is associated with various autoimmune diseases, yet its impact on B cells remains unexplored.
Objective: This study investigated the direct effects of Fli1 depletion on B cell populations, focusing on age-associated B cells (ABCs).
Methods: Splenocytes of Fli1 BcKO (Cd19-Cre; Fli1) and Cd19-Cre mice were analyzed flow cytometrically.
Exp Cell Res
January 2025
Cardiovascular Center, College of Medicine, University of Cincinnati, Ohio-45267, United States of America; School of Chemical and Biotechnology, SASTRA Deemed University, Tirumalaisamudram, Thanjavur-613401, Tamil Nadu, India. Electronic address:
Multiple forms of cell death contribute significantly to cardiovascular pathologies, negatively impacting cardiac remodeling and leading to heart failure. While myocardial cell death has been associated with PM induced cardiotoxicity, the temporal dynamics of various cell death forms, such as apoptosis, ferroptosis, necroptosis, and pyroptosis, in relation to inflammatory processes, remain underexplored. This study examines the time-dependent onset and progression of these cell death pathways in the myocardium and their correlation with inflammation in a Wistar rat model.
View Article and Find Full Text PDFInt J Biol Macromol
January 2025
Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou 510280, Guangdong, China. Electronic address:
R-loops, three-stranded nucleic acid structures composed of RNA-DNA hybrids, are increasingly recognized as central regulators of genomic stability and transcription. These structures play critical roles across various cellular processes, including DNA replication, repair, and gene regulation, with significant implications for stem cell biology and disease pathogenesis. This review comprehensively explores the molecular underpinnings of R-loop formation, emphasizing the dual nature of R-loops in both facilitating normal cellular functions and contributing to genomic instability.
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