Visual feature extraction from dermoscopic colour images for classification of melanocytic skin lesions

The early diagnosis of Melanoma is a challenging task for dermatologists, because of the characteristic similarities of Melanoma with other skin lesions such as typical moles and dysplastic nevi. Aims: This work aims to help both experienced and non-experienced dermatologists in the early detection of cutaneous Melanoma through the development of a computational helping tool based on the “ABCD” rule of dermoscopy. Moreover, it aims to decrease the need for invasive biopsy procedure for each tested abnormal skin lesion. Methods: This is accomplished through the utilization of MATLAB programming language to build a feature extraction tool for the assessment of lesion asymmetry, borders irregularity, and colors variation in the tested lesion. Results: The helping tool obtained a sensitivity of 81.48%, a specificity of 52.83% and accuracy of 62.50% in the assessment of the Asymmetry Index. A new metric for the borders irregularity index was built. Finally, for the Colors Variation Index algorithm a sensitivity of 51.37%, a specificity of 61.51% and accuracy of 57.80% was achieved. Conclusions: This work created a computational tool based on the ABCD-rule, which is helpful for both experienced and non-experienced dermatologists in the early discrimination of Melanoma than other types of skin lesions and to eliminate the need of the biopsy procedure. A new metric for the Borders Irregularity Index was established depending on the number of inflection points in the lesion’s borders

Binding of Transcription Factor GabR to DNA Requires Recognition of DNA Shape at a Location Distinct from its Cognate Binding Site

Mechanisms for transcription factor recognition of specific DNA base sequences are well characterized and recent studies demonstrate that the shape of these cognate binding sites is also important. Here, we uncover a new mechanism where the transcription factor GabR simultaneously recognizes two cognate binding sites and the shape of a 29 bp DNA sequence that bridges these sites. Small-angle X-ray scattering and multi-angle laser light scattering are consistent with a model where the DNA undergoes a conformational change to bend around GabR during binding. In silico predictions suggest that the bridging DNA sequence is likely to be bendable in one direction and kinetic analysis of mutant DNA sequences with biolayer interferometry, allowed the independent quantification of the relative contribution of DNA base and shape recognition in the GabR–DNA interaction. These indicate that the two cognate binding sites as well as the bendability of the DNA sequence in between these sites are required to form a stable complex. The mechanism of GabR–DNA interaction provides an example where the correct shape of DNA, at a clearly distinct location from the cognate binding site, is required for transcription factor binding and has implications for bioinformatics searches for novel binding sites