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Yayın Discovering cis-regulatory modules by optimizing barbecues(Elsevier Science Bv, 2009-05-28) Mosig, Axel; Bıyıkoğlu, Türker; Prohaska, Sonja J.; Stadler, Peter F.Gene expression in eukaryotic cells is regulated by a complex network of interactions, in which transcription factors and their binding sites on the genomic DNA play a determining role. As transcription factors rarely, if ever, act in isolation, binding sites of interacting factors are typically arranged in close proximity forming so-called cis-regulatory modules. Even when the individual binding sites are known, module discovery remains a hard combinatorial problem, which we formalize here as the Best Barbecue Problem. It asks for simultaneously stabbing a maximum number of differently colored intervals from K arrangements of colored intervals. This geometric problem turns out to be an elementary, yet previously unstudied combinatorial optimization problem of detecting common edges in a family of hypergraphs, a decision version of which we show here to be NP-complete. Due to its relevance in biological applications, we propose algorithmic variations that are suitable for the analysis of real data sets comprising either many sequences or many binding sites. Being based on set systems induced by interval arrangements, our problem setting generalizes to discovering patterns of co-localized itemsets in non-sequential objects that consist of corresponding arrangements or induce set systems of co-localized items. In fact, our optimization problem is a generalization of the popular concept of frequent itemset mining.Yayın Tectonic and climatic controls on Quaternary fluvial processes and river terrace formation in a Mediterranean setting, the Goksu River, southern Turkey(Cambridge University Press, 2019-03) Avşin Görendağlı, Nurcan; Vandenberghe, Jef; Van Balen, Ronald; Güneç Kıyak, Nafiye; Öztürk, TuğbaClimate and tectonics effect the fluvial evolution of the Mediterranean Mut basin. The basin contains a river terrace staircase of 16 levels (T16-T1) ranging from 365 to 10m above the current Goksu River in its middle and lower sections. These river terraces records tectonic uplift in the Mut basin. Optically stimulated luminescence (OSL) dating of the fluvial sediments of the youngest terrace (T16) provides a chronology for the assessment of the important impacts of climatic changes. The ages from the youngest river terrace deposits in T16 may be subdivided into two intervals: (1) 239-194.7 ka during the later part of Marine Oxygen Isotope Stage (MIS) 7, implying that the aggradation of T16 started in (the final phase of) this warm period; and (2) 187.9-171 ka during much of MIS 6. Thus, it appears that the Goksu River continued depositing sediment from an interglacial into a glacial time. The differences in climate-driven fluvial evolution between this Mediterranean fluvial system and the classical, well-studied temperate-periglacial river systems in Europe may be the result of different vegetation cover and greater thaw of more intense snowfalls.Yayın Free software, business capital, and institutional change: a veblenian analysis of the software industry(M. E. Sharpe Inc, 2012-12) Koloğlugil, Serhat; Koloğlugil, SerhatFree software, unlike proprietary software under exclusive copyright control, exemplifies a form of productive and innovative activity that is based upon mutual sharing of technological knowledge. Free software engineers, who get connected through various software-development projects, voluntarily contribute their time and skills to produce computer programs which, they insist, should be free for anyone to use, modify, and distribute. This paper argues that Thorstein Veblen's socio-economic theory - in particular his conceptions of capital, technological knowledge and institutional change - offers a fruitful framework to analyze the emergence of free software as an economic and social phenomenon. From the Veblenian perspective, the free software movement argues that the technological knowledge in the software industry should freely be available to society as a part of its common stock of knowledge. In other words, they are against the use of copyright law as a predatory strategy by software corporations, while the current technological conditions in the software industry allow for an institutional arrangement of production and innovation based on cooperative habits of thought.
