On finding minimal absent words

<p>Abstract</p> <p>Background</p> <p>The problem of finding the shortest absent words in DNA data has been recently addressed, and algorithms for its solution have been described. It has been noted that longer absent words might also be of interest, but the existing algorithms only provide generic absent words by trivially extending the shortest ones.</p> <p>Results</p> <p>We show how absent words relate to the repetitions and structure of the data, and define a new and larger class of absent words, called minimal absent words, that still captures the essential properties of the shortest absent words introduced in recent works. The words of this new class are minimal in the sense that if their leftmost or rightmost character is removed, then the resulting word is no longer an absent word. We describe an algorithm for generating minimal absent words that, in practice, runs in approximately linear time. An implementation of this algorithm is publicly available at <url>ftp://www.ieeta.pt/~ap/maws</url>.</p> <p>Conclusion</p> <p>Because the set of minimal absent words that we propose is much larger than the set of the shortest absent words, it is potentially more useful for applications that require a richer variety of absent words. Nevertheless, the number of minimal absent words is still manageable since it grows at most linearly with the string size, unlike generic absent words that grow exponentially. Both the algorithm and the concepts upon which it depends shed additional light on the structure of absent words and complement the existing studies on the topic.</p

FGF-2, TGF&#946;-1, PDGF-A and respective receptors expression in pleomorphic adenoma myoepithelial cells: an in vivo and in vitro study

Myoepithelial cells have an important role in salivary gland tumor development, contributing to a low grade of aggressiveness of these tumors. Normal myoepithelial cells are known by their suppressor function presenting increased expression of extracellular matrix genes and protease inhibitors. The importance of stromal cells and growth factors during tumor initiation and progression has been highlighted by recent literature. Many tumors result from the alteration of paracrine growth factors pathways. Growth factors mediate a wide variety of biological processes such as development, tissue repair and tumorigenesis, and also contribute to cellular proliferation and transformation in neoplastic cells. OBJECTIVES: This study evaluated the expression of fibroblast growth factor-2 (FGF-2), transforming growth factor &#946;-1 (TGF&#946;-1), platelet-derived growth factor-A (PDGF-A) and their respective receptors (FGFR-1, FGFR-2, TGF&#946;R-II and PDGFR-&#945;) in myoepithelial cells from pleomorphic adenomas (PA) by in vivo and in vitro experiments. MATERIAL AND METHODS: Serial sections were obtained from paraffin-embedded PA samples obtained from the school's files. Myoepithelial cells were obtained from explants of PA tumors provided by surgery from different donors. Immunohistochemistry, cell culture and immunofluorescence assays were used to evaluate growth factor expression. RESULTS: The present findings demonstrated that myoepithelial cells from PA were mainly positive to FGF-2 and FGFR-1 by immunohistochemistry and immunofluorescence. PDGF-A and PDGFR-&#945; had moderate expression by immunohistochemistry and presented punctated deposits throughout cytoplasm of myoepithelial cells. FGFR-2, TGF&#946;-1 and TGF&#946;R-II were negative in all samples. CONCLUSIONS: These data suggested that FGF-2 compared to the other studied growth factors has an important role in PA benign myoepithelial cells, probably contributing to proliferation of these cells through the FGFR-1