Considering Abundance, Affinity, and Binding Site Availability in the NF-κB Target Selection Puzzle

The NF-κB transcription regulation system governs a diverse set of responses to various cytokine stimuli. With tools from in vitro biochemical characterizations, to omics-based whole genome investigations, great strides have been made in understanding how NF-κB transcription factors control the expression of specific sets of genes. Nonetheless, these efforts have also revealed a very large number of potential binding sites for NF-κB in the human genome, and a puzzle emerges when trying to explain how NF-κB selects from these many binding sites to direct cell-type- and stimulus-specific gene expression patterns. In this review, we surmise that target gene transcription can broadly be thought of as a function of the nuclear abundance of the various NF-κB dimers, the affinity of NF-κB dimers for the regulatory sequence and the availability of this regulatory site. We use this framework to place quantitative information that has been gathered about the NF-κB transcription regulation system into context and thus consider questions it answers, and questions it raises. We end with a brief discussion of some of the future prospects that new approaches could bring to our understanding of how NF-κB transcription factors orchestrate diverse responses in different biological contexts

A Counterexample Regarding Labelled Well-Quasi-Ordering

Korpelainen, Lozin, and Razgon conjectured that a hereditary property of graphs which is well-quasi-ordered by the induced subgraph order and defined by only finitely many minimal forbidden induced subgraphs is labelled well-quasi-ordered, a notion stronger than that of n-well-quasi-order introduced by Pouzet in the 1970s. We present a counterexample to this conjecture. In fact, we exhibit a hereditary property of graphs which is well-quasi-ordered by the induced subgraph order and defined by finitely many minimal forbidden induced subgraphs yet is not 2-well-quasi-ordered. This counterexample is based on the widdershins spiral, which has received some study in the area of permutation patterns

Governance tools for board members : adapting strategy maps and balanced scorecards for directorial action

The accountability of members of the board of directors of publicly traded companies has increased over years. Corresponding to these developments, there has been an inadequate advancement of tools and frameworks to help directorial functioning. This paper provides an argument for design of the Balanced Scorecard and Strategy Maps made available to the directors as a means of influencing, monitoring, controlling and assisting managerial action. This paper examines how the Balanced Scorecard and Strategy Maps could be modified and used for this purpose. The paper suggests incorporating Balanced Scorecards in the Internal Process perspective, ‘internal’ implying here not just ‘internal to the firm’, but also ‘internal to the inter-organizational system’. We recommend that other such factors be introduced separately under a new ‘perspective’ depending upon what the board wants to emphasize without creating any unwieldy proliferation of measures. Tracking the Strategy Map over time by the board of directors is a way for the board to take responsibility for the firm’s performance. The paper makes a distinction between action variables and monitoring variables. Monitoring variables are further divided on the basis of two considerations: a) whether results have been met or not and b) whether causative factors have met the expected levels of performance or not. Based on directorial responsibilities and accountability, we take another look at how the variables could be specified more completely and accurately with directorial recommendations for executives

VISUAL PPINOT: A Graphical Notation for Process Performance Indicators

Process performance indicators (PPIs) allow the quantitative evaluation of business processes, providing essential information for decision making. It is common practice today that business processes and PPIs are usually modelled separately using graphical notations for the former and natural language for the latter. This approach makes PPI definitions simple to read and write, but it hinders maintenance consistency between business processes and PPIs. It also requires their manual translation into lower-level implementation languages for their operationalisation, which is a time-consuming, error-prone task because of the ambiguities inherent to natural language definitions. In this article, Visual ppinot, a graphical notation for defining PPIs together with business process models, is presented. Its underlying formal metamodel allows the automated processing of PPIs. Furthermore, it improves current state-of-the-art proposals in terms of expressiveness and in terms of providing an explicit visualisation of the link between PPIs and business processes, which avoids inconsistencies and promotes their co-evolution. The reference implementation, developed as a complete tool suite, has allowed its validation in a multiple-case study, in which five dimensions of Visual ppinot were studied: expressiveness, precision, automation, understandability, and traceability

Decomposing simple permutations, with enumerative consequences

We prove that every sufficiently long simple permutation contains two long almost disjoint simple subsequences, and then we show how this result has enumerative consequences. For example, it implies that, for any r, the number of permutations with at most r copies of 132 has an algebraic generating function (this was previously proved, constructively, by Bóna and (independently) Mansour and Vainshtein)

Product costing in service organizations

Conventional wisdom and empirical evidence suggest that in manufacturing businesses product costs are used for various purposes, including inventory valuation, product pricing and mix decisions and for management planning and control. In this paper the validity of these three specific uses in the service sector are explored in five large for profit service organizations. The first of our three conclusions is that inventory valuation was not a major issue in these five service organizations, as the inherent perishability of their services mean that they cannot be stored. Second, only two of the five organizations used full product costs for pricing decisions. Third, in all five organizations costs were planned and controlled via responsibility centres linked to functional activities rather than products/services, which did not seem to be a useful unit of analysis. This paper suggests that a closer alignment of a service organization's responsibility centres with its value chain might be a source of competitive advantage, and that more case study research is needed in this area