We have developed an algorithm ("Lever") that systematically maps metazoan DNA regulatory motifs or motif combinations to the sets of genes that they likely regulate. Lever accomplishes this by assessing whether the motifs are enriched within cis regulatory modules (CRMs), predicted by our "PhylCRM" algorithm, in the noncoding sequences surrounding genes in a collection of gene sets. When these gene sets correspond to Gene Ontology (GO) categories, the results of Lever analysis allow the unbiased assignment of functional annotations to the regulatory motifs and also to the candidate CRMs that comprise the genomic motif occurrences. We demonstrate these methods using human myogenic differentiation as a model system, for which we statistically assessed greater than 25,000 pairings of gene sets and motifs / motif combinations. These results allowed us to assign functional annotations to candidate regulatory motifs predicted previously, and to identify gene sets that are likely to be co-regulated via shared regulatory motifs. Lever allows moving beyond the identification of putative regulatory motifs in mammalian genomes, towards understanding their biological roles. This approach is general and can be applied readily to any cell type, gene expression pattern, or organism of interest.
Results from this study indicate that the performance of template matching is comparable with or better than that of manual tumor localization. This study serves as preliminary investigations towards developing online motion tracking techniques for hybrid MRI-Linac systems. Accuracy of template matching makes it a suitable candidate to replace the labor intensive manual tumor localization for obtaining the ground truth when testing other motion management techniques.
Purpose
Quantitative Cone Beam CT (CBCT) imaging is increasing in demand for precise image‐guided radiotherapy because it provides a foundation for advanced image‐guided techniques, including accurate treatment setup, online tumor delineation, and patient dose calculation. However, CBCT is currently limited only to patient setup in the clinic because of the severe issues in its image quality. In this study, we develop a learning‐based approach to improve CBCT's image quality for extended clinical applications.
Materials and methods
An auto‐context model is integrated into a machine learning framework to iteratively generate corrected CBCT (CCBCT) with high‐image quality. The first step is data preprocessing for the built training dataset, in which uninformative image regions are removed, noise is reduced, and CT and CBCT images are aligned. After a CBCT image is divided into a set of patches, the most informative and salient anatomical features are extracted to train random forests. Within each patch, alternating RF is applied to create a CCBCT patch as the output. Moreover, an iterative refinement strategy is exercised to enhance the image quality of CCBCT. Then, all the CCBCT patches are integrated to reconstruct final CCBCT images.
Results
The learning‐based CBCT correction algorithm was evaluated using the leave‐one‐out cross‐validation method applied on a cohort of 12 patients’ brain data and 14 patients’ pelvis data. The mean absolute error (MAE), peak signal‐to‐noise ratio (PSNR), normalized cross‐correlation (NCC) indexes, and spatial nonuniformity (SNU) in the selected regions of interest (ROIs) were used to quantify the proposed algorithm's correction accuracy and generat the following results: mean MAE = 12.81 ± 2.04 and 19.94 ± 5.44 HU, mean PSNR = 40.22 ± 3.70 and 31.31 ± 2.85 dB, mean NCC = 0.98 ± 0.02 and 0.95 ± 0.01, and SNU = 2.07 ± 3.36% and 2.07 ± 3.36% for brain and pelvis data.
Conclusion
Preliminary results demonstrated that the novel learning‐based correction method can significantly improve CBCT image quality. Hence, the proposed algorithm is of great potential in improving CBCT's image quality to support its clinical utility in CBCT‐guided adaptive radiotherapy.
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