Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik

Permanent URI for this collectionhttps://hdl.handle.net/11147/9

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  • 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.
  • Article
    Citation - WoS: 6
    Citation - Scopus: 3
    Determining Element Accumulations in Turkish Red Pine Used as a Bioindicator for Estimating of Existing Pollution on Both Sides of Bosphorus in İstanbul
    (Parlar Scientific Publications, 2020) Yalçın, İbrahim Ertuğrul; Özyiğit, İbrahim İlker; Doğan, İlhan; Demir, Göksel; Yarcı, Celal
    Evergreen Turkish red pine tree shows wide distribution around Aegean and Mediterranean regions in Turkey. Herein work investigated the mineral nutrient status of Turkish red pine as a bioindicator for revealing the impact of existing pollution on both sides of Bosphorus in Istanbul. For this, Al, B, Ca, Cu, Fe, K, Mg, Na and Zn concentrations were determined in unwashed and washed leaves and barks of the plant and soil samples. The standard procedures were applied and the determinations of element concentrations in all samples were done using ICP-OES. The sample collections were performed at five different locations in Istanbul, 4 from the Bosphorus region and one from Prince Island (as control). The highest element concentrations (in mg kg(-1) DW) in plant parts were recorded between 109.10 +/- 1.68 and 120.58 +/- 1.75 for Al, 10.18 +/- 0.14 and 12.52 +/- 0.17 for B, 8765.42 +/- 92.41 and 9600.69 +/- 102.22 for Ca, 10.91 +/- 0.13 and 11.73 +/- 0.16 for Cu, 226.85 +/- 3.01 and 254.07 +/- 3.20 for Fe, 4050.69 +/- 48.51 and 4477.08 +/- 52.34 for K, 794.58 +/- 9.82 and 878.33 +/- 10.07 for Mg, 1255.14 +/- 14.67 and 1374.31 +/- 18.55 for Na and 34.92 +/- 0.49 and 37.25 +/- 0.57 for Zn while the highest element concentrations (in mg kg(-1) DW) in co-located soil samples were measured between 5470.42 +/- 66.48 and 6046.25 +/- 73.54 for Al, 14.86 +/- 0.20 and 16.43 +/- 0.29 for B, 4600.56 +/- 55.22 and 4984.86 +/- 62.71 for Ca, 22.33 +/- 0.36 and 25.07 +/- 0.48 for Cu, 5500.01 +/- 71.05 and 5953.06 +/- 80.16 for Fe, 1819.44 +/- 23.51 and 2029.17 +/- 27.04 for K, 4108.75 +/- 50.77 and 4714.17 +/- 58.09 for Mg, 111.11 +/- 1.82 and 122.08 +/- 2.45 for Na and 117.10 +/- 2.33 and 126.86 +/- 2.61 for Zn.