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Long-patch Base Excision Repair

Since the discovery of the two BER pathways, there has been a debate about how a cell chooses one pathway over the other and the factors determining this selection. Numerous in vitro experiments have pointed out multiple determinants for the sub-pathway selection. These are:
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The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...
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Related Experiment Video

Updated: May 11, 2026

From Voxels to Knowledge: A Practical Guide to the Segmentation of Complex Electron Microscopy 3D-Data
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Predicting the Effort Required to Manually Mend Auto-Segmentations.

Da He, Yubing Tong, Drew A Torigian

    IEEE Journal of Biomedical and Health Informatics
    |October 23, 2025
    PubMed
    Summary
    This summary is machine-generated.

    Evaluating auto-segmentation in clinical practice requires assessing manual correction effort. New deep learning models can predict this effort directly from images and auto-segmentations, improving clinical efficiency.

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    Area of Science:

    • Medical Imaging
    • Artificial Intelligence
    • Radiation Oncology

    Background:

    • Auto-segmentation accuracy is crucial for clinical utility.
    • Existing metrics like Dice Coefficient (DC) and Hausdorff Distance (HD) fail to capture manual correction effort.
    • Clinical efficiency requires evaluating the time experts spend mending auto-segmentations.

    Purpose of the Study:

    • To explore methods for evaluating auto-segmentations considering clinical efficiency.
    • To assess explicit metrics and novel deep learning approaches for predicting manual mending effort.
    • To validate these methods across multiple institutions and organs for radiation therapy planning.

    Main Methods:

    • Recorded expert correction time to establish ground-truth mending effort.
    • Evaluated five explicit metrics, including Mendability Index (MIhd) and spatial Hausdorff Distance (sHD).
    • Developed and tested deep learning networks to implicitly predict mending effort using auto-segmentations and original images.

    Main Results:

    • MIhd best predicted mending effort for sparse objects (6.2-14.4% error).
    • sHD performed best for large, non-sparse objects.
    • Deep learning models accurately predicted mending effort (2.9-12.9% error) without needing ground-truth segmentations.

    Conclusions:

    • Explicit metrics have limitations in predicting clinical mending effort.
    • Deep learning offers a promising approach to predict mending effort implicitly and efficiently.
    • Effort-predicting deep models can assess clinical usability beyond technical evaluations.