Mueller, J. L. | Search bioRxiv

bioRxiv2018

Development of algorithms for automated detection of cervical pre-cancers with a low-cost, point-of-care, Pocket Colposcope

GoalIn this work, we propose methods for (1) automatic feature extraction and classification for acetic acid and Lugols iodine cervigrams and (2) methods for combining features/diagnosis of different contrasts in cervigrams for improved performance.\n\nMethodsWe developed algorithms to pre-process pathology-labeled cervigrams and to extract simple but powerful color and textural-based features. The features were used to train a support vector machine model to classify cervigrams based on corresponding pathology for visual inspection with acetic acid, visual inspection with Lugols iodine, and a combination of the two contrasts.\n\nResultsThe proposed framework achieved a sensitivity, specificity, and accuracy of 81.3%, 78.6%, and 80.0%, respectively when used to distinguish cervical intraepithelial neoplasia (CIN+) relative to normal and benign tissues. This is superior to the average values achieved by three expert physicians on the same data set for discriminating normal/benign cases from CIN+ (77% sensitivity, 51% specificity, 63% accuracy).\n\nConclusionThe results suggest that utilizing simple color- and textural-based features from visual inspection with acetic acid and visual inspection with Lugols iodine images may provide unbiased automation of cervigrams.\n\nSignificanceThis would enable automated, expert-level diagnosis of cervical pre-cancer at the point-of-care.

bioinformatics↗

bioRxiv2018

Male mice with large inversions or deletions of X-palindrome arms are fertile and express their associated genes post-meiosis.

Large (>10 kb) palindromic sequences are enriched on mammalian sex chromosomes. In mice, these palindromes harbor gene families ([≥]2 gene copies) expressed exclusively in post-meiotic testicular germ cells, at a time when most single-copy sex-linked genes are transcriptionally repressed. This distinct expression pattern led to the hypothesis that containment within palindrome structures or having [≥]2 gene enables post-meiotic gene expression. We tested these two hypotheses by using CRISPR to precisely engineer large (10s of kb) inversions and deletions of X chromosome palindrome arms for two regions carrying the mouse 4930567H17Rik and Mageb5 gene families. We found that 4930567H17Rik and Mageb5 gene expression is unaffected in mice carrying palindrome arm inversions, suggesting that palindromic structure is not important for mediating palindrome-associated gene expression. We also found that 4930567H17Rik and Mageb5 gene expression is reduced by half in mice carrying palindrome arm deletions, allowing us to test whether palindrome-associated genes are sensitive to reduced expression levels resulting in spermatogenic defects. Male mice carrying palindrome arm deletions of 4930567H17Rik or Mageb5, however, are fertile, have normal testis histology, and show no aberrations in spermatogenic cell population frequencies via FACS quantification. Together, these findings suggest that large palindromic structures on the sex chromosomes are not necessary for their associated genes to evade post-meiotic transcriptional repression and that these genes are not sensitive to reduced expression levels. Large sex chromosome palindromes may thus be important for other reasons, such as the long-term evolutionary stability of their associated gene families.

genetics↗