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Collagen

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ColGen: An end-to-end deep learning model to predict thermal stability of de novo collagen sequences.

Journal of the mechanical behavior of biomedical materials
Collagen is the most abundant structural protein in humans, with dozens of sequence variants accounting for over 30% of the protein in an animal body. The fibrillar and hierarchical arrangements of collagen are critical in providing mechanical proper...

Spatial and temporal dynamics of RhoA activities of single breast tumor cells in a 3D environment revealed by a machine learning-assisted FRET technique.

Experimental cell research
One of the hallmarks of cancer cells is their exceptional ability to migrate within the extracellular matrix (ECM) for gaining access to the circulatory system, a critical step of cancer metastasis. RhoA, a small GTPase, is known to be a key molecula...

Structural, functional and molecular pathogenesis of pelvic organ prolapse in patient and deficient mice.

Aging
Pelvic organ prolapse is a worldwide health problem to elderly women. Understanding its pathogenesis and an ideal animal model are crucial to developing promising treatments. The present study aimed to investigate new clinical significance and detail...

Deep learning identification of stiffness markers in breast cancer.

Biomaterials
While essential to our understanding of solid tumor progression, the study of cell and tissue mechanics has yet to find traction in the clinic. Determining tissue stiffness, a mechanical property known to promote a malignant phenotype in vitro and in...

Predicting and understanding arterial elasticity from key microstructural features by bidirectional deep learning.

Acta biomaterialia
Microstructural features and mechanical properties are closely related in all soft biological tissues. Both yet exhibit considerable inter-individual differences and are affected by factors such as aging and disease and its progression. Histological ...

Discovering design principles of collagen molecular stability using a genetic algorithm, deep learning, and experimental validation.

Proceedings of the National Academy of Sciences of the United States of America
Collagen is the most abundant structural protein in humans, providing crucial mechanical properties, including high strength and toughness, in tissues. Collagen-based biomaterials are, therefore, used for tissue repair and regeneration. Utilizing col...

CollagenTransformer: End-to-End Transformer Model to Predict Thermal Stability of Collagen Triple Helices Using an NLP Approach.

ACS biomaterials science & engineering
Collagen is one of the most important structural proteins in biology, and its structural hierarchy plays a crucial role in many mechanically important biomaterials. Here, we demonstrate how transformer models can be used to predict, directly from the...

Mesoscopic structural analysis via deep learning processing, with a special reference to in vitro alteration in collagen fibre induced by a gap junction inhibitor.

Microscopy (Oxford, England)
Dense connective tissue, including the ligament, tendon, fascia and cornea, is formed by regularly arranged collagen fibres synthesized by fibroblasts (Fbs). The mechanism by which fibre orientation is determined remains unclear. Periodontal ligament...

Collagen fiber centerline tracking in fibrotic tissue via deep neural networks with variational autoencoder-based synthetic training data generation.

Medical image analysis
The role of fibrillar collagen in the tissue microenvironment is critical in disease contexts ranging from cancers to chronic inflammations, as evidenced by many studies. Quantifying fibrillar collagen organization has become a powerful approach for ...

Multimodal characterization of the collagen hydrogel structure and properties in response to physiologically relevant pH fluctuations.

Acta biomaterialia
pH fluctuations within the extracellular matrix (ECM) and its principal constituent collagen, particularly in solid tumors and chronic wounds, may influence its structure and function. Whereas previous research examined the impact of pH on collagen f...