Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection

Permanent URI for this collectionhttps://hdl.handle.net/11147/7148

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Subject: search.filters.subject.Wound healing

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  • Article
    Novel Neural Style Transfer Based Data Synthesis Method for Phase-Contrast Wound Healing Assay Images
    (Elsevier Ltd, 2024) Erdem,Y.S.; Iheme,L.O.; Uçar,M.; Özuysal,Ö.Y.; Balıkçı,M.; Morani,K.; Ünay,D.
    Recent advancements in the field of image synthesis have led to the development of Neural Style Transfer (NST) and Generative Adversarial Networks (GANs) which have proven to be powerful tools for data augmentation and realistic data generation. While GANs have been widely used for both data augmentation and generation, NST has not been employed for data generation tasks. Nonetheless, the simpler structure of NST compared to GANs makes it a promising alternative. In this research, we introduce an NST-based method for data generation, which to the best of our knowledge, is the first of its kind. By taking advantage of simplified architecture of NST models attributed to the utilization of a real image as the style input, our method enhances performance in data generation tasks under limited resource conditions. Additionally by utilizing patch-based training and high-resolution inference process high quality images are synthesized with limited resources. Furthermore multi-model and noised input is utilized for increased diversity with the novel NST-based data generation approach. Our proposed method utilizes binary segmentation maps as the condition input, representing the cell and wound regions. We evaluate the performance of our proposed NST-based method and compare it with a modified and fine-tuned conditional GAN (C-GAN) methods for the purpose of conditional generation of phase-contrast wound healing assay images. Through a series of quantitative and qualitative analyses, we demonstrate that our NST-based method outperforms the modified C-GAN while utilizing fewer resources. Additionally, we show that our NST-based method enhances segmentation performance when used as a data augmentation method. Our findings provide compelling evidence regarding the potential of NST for data generation tasks and its superiority over traditional GAN-based methods. The NST for data generation method was implemented in Python language and will be accessible at https://github.com/IDU-CVLab/NST_for_Gen under the MIT licence. © 2024 Elsevier Ltd
  • Article
    Citation - WoS: 8
    Citation - Scopus: 8
    Canonical Wnt and Tgf-β/Bmp Signaling Enhance Melanocyte Regeneration but Suppress Invasiveness, Migration, and Proliferation of Melanoma Cells
    (Frontiers Media S.A., 2023) Katkat, Esra; Demirci, Yeliz; Heger, Guillaume; Karagülle, Doğa; Papatheodorou, Irene; Brazma, Alvis; Özhan, Güneş
    Melanoma is the deadliest form of skin cancer and develops from the melanocytes that are responsible for the pigmentation of the skin. The skin is also a highly regenerative organ, harboring a pool of undifferentiated melanocyte stem cells that proliferate and differentiate into mature melanocytes during regenerative processes in the adult. Melanoma and melanocyte regeneration share remarkable cellular features, including activation of cell proliferation and migration. Yet, melanoma considerably differs from the regenerating melanocytes with respect to abnormal proliferation, invasive growth, and metastasis. Thus, it is likely that at the cellular level, melanoma resembles early stages of melanocyte regeneration with increased proliferation but separates from the later melanocyte regeneration stages due to reduced proliferation and enhanced differentiation. Here, by exploiting the zebrafish melanocytes that can efficiently regenerate and be induced to undergo malignant melanoma, we unravel the transcriptome profiles of the regenerating melanocytes during early and late regeneration and the melanocytic nevi and malignant melanoma. Our global comparison of the gene expression profiles of melanocyte regeneration and nevi/melanoma uncovers the opposite regulation of a substantial number of genes related to Wnt signaling and transforming growth factor beta (TGF-beta)/(bone morphogenetic protein) BMP signaling pathways between regeneration and cancer. Functional activation of canonical Wnt or TGF-beta/BMP pathways during melanocyte regeneration promoted melanocyte regeneration but potently suppressed the invasiveness, migration, and proliferation of human melanoma cells in vitro and in vivo. Therefore, the opposite regulation of signaling mechanisms between melanocyte regeneration and melanoma can be exploited to stop tumor growth and develop new anti-cancer therapies.
  • Book Part
    Citation - Scopus: 1
    Automated Analysis of Phase-Contrast Optical Microscopy Time-Lapse Images: Application To Wound Healing and Cell Motility Assays of Breast Cancer
    (Elsevier, 2023) Erdem, Yusuf Sait; Ayanzadeh, Aydın; Mayalı, Berkay; Balıkçı, Muhammed; Belli, Özge Nur; Uçar, Mahmut; Yalçın Özuysal, Özden; Pesen Okvur, Devrim; Önal, Sevgi; Morani, Kenan; Iheme, Leonardo Obinna; Töreyin, Behçet Uğur
    This chapter describes a workflow for analyzing phase-contrast microscopy (PCM) data from two fundamental types of biomedical assays: assays for cell motility and assays for wound healing. The workflow of the analysis is composed of the methods for acquiring, restoring, segmenting, and quantifying biomedical data. In the literature, there have been separate methods aimed at specific stages of PCM data analysis. Nonetheless, there has never been a complete workflow for all stages of analysis. This work is an innovation that proposes an end-to-end workflow for image pre-processing, deep learning segmentation, tracking, and quantification stages in cell motility and wound healing assay analyses. The findings indicate that domain knowledge can be used to make simple but significant improvements to the results of cutting-edge methods. Furthermore, even for deep learning-based methods, pre-processing is clearly a necessary step in the workflow. © 2023 Elsevier Inc. All rights reserved.
  • Conference Object
    Citation - Scopus: 2
    Yara İyileşmesi Mikroskopi Görüntü Serilerinin Otomatik Analizi - Bir Ön-çalışma
    (IEEE, 2020) Mayalı, Berkay; Şaylığ, Orkun; Yalçın Özuysal, Özden; Pesen Okvur, Devrim; Töreyin, Behçet Uğur; Ünay, Devrim
    Collective cell analysis from microscopy image series is important for wound healing research. Computer-based automation of such analyses may help in rapid acquisition of reliable and reproducible results. In this study phase -contrast optical microscopy image series of an in-vitro wound healing essay is manually delineated by two experts and its analysis is realized, traditional image processing and deep learning based approaches for automated segmentation of wound area are developed and their perlOrmance comparisons are carried out.
  • Article
    Citation - WoS: 17
    Citation - Scopus: 17
    Developing Wound Dressings Using 2-Deoxy To Induce Angiogenesis as a Backdoor Route for Stimulating the Production of Vascular Endothelial Growth Factor
    (MDPI Multidisciplinary Digital Publishing Institute, 2021) Dikici, Serkan; Yar, Muhammad; Bullock, Anthony J.; Shepherd, Joanna; Roman, Sabiniano; MacNeil, Sheila
    2-deoxy-D-Ribose (2dDR) was first identified in 1930 in the structure of DNA and discovered as a degradation product of it later when the enzyme thymidine phosphorylase breaks down thymidine into thymine. In 2017, our research group explored the development of wound dressings based on the delivery of this sugar to induce angiogenesis in chronic wounds. In this review, we will survey the small volume of conflicting literature on this and related sugars, some of which are reported to be anti-angiogenic. We review the evidence of 2dDR having the ability to stimulate a range of pro-angiogenic activities in vitro and in a chick pro-angiogenic bioassay and to stimulate new blood vessel formation and wound healing in normal and diabetic rat models. The biological actions of 2dDR were found to be 80 to 100% as effective as VEGF in addition to upregulating the production of VEGF. We then demonstrated the uptake and delivery of the sugar from a range of experimental and commercial dressings. In conclusion, its pro-angiogenic properties combined with its improved stability on storage compared to VEGF, its low cost, and ease of incorporation into a range of established wound dressings make 2dDR an attractive alternative to VEGF for wound dressing development.