Markov chain aggregation and its application to rule-based modelling

Rule-based modelling allows to represent molecular interactions in a compact and natural way. The underlying molecular dynamics, by the laws of stochastic chemical kinetics, behaves as a continuous-time Markov chain. However, this Markov chain enumerates all possible reaction mixtures, rendering the analysis of the chain computationally demanding and often prohibitive in practice. We here describe how it is possible to efficiently find a smaller, aggregate chain, which preserves certain properties of the original one. Formal methods and lumpability notions are used to define algorithms for automated and efficient construction of such smaller chains (without ever constructing the original ones). We here illustrate the method on an example and we discuss the applicability of the method in the context of modelling large signalling pathways

A falling of the veils: turning points and momentous turning points in leadership and the creation of CSR

This article uses the life stories approach to leadership and leadership development. Using exploratory, qualitative data from a Forbes Global 2000 and FTSE 100 company, we discuss the role of the turning point (TP) as an important antecedent of leadership in corporate social responsibility. We argue that TPs are causally efficacious, linking them to the development of life narratives concerned with an evolving sense of personal identity. Using both a multi-disciplinary perspective and a multi-level focus on CSR leadership, we identify four narrative cases. We propose that they helped to re-define individuals’ sense of self and in some extreme cases completely transformed their self-identity as leaders of CSR. Hence we also distinguish the momentous turning point (MTP) that created a seismic shift in personality, through re-evaluation of the individuals’ personal values. We argue that whilst TPs are developmental experiences that can produce responsible leadership, the MTP changes the individuals’ personal priorities in life to produce responsible leadership that perhaps did not exist previously. Thus we appropriate Maslow’s (1976, p. 77) metaphorical phrase ‘A falling of the veils’ from his discussion of peak and desolation experiences that produce personal growth. Using a multi-disciplinary literature from social theory (Archer, 2012) moral psychology (Narvaez, 2009) and social psychology (Schwartz, 2010), we present a theoretical model that illustrates the psychological process of the (M)TP, thus contributing to the growing literature on the microfoundations of CSR

Current approaches to gene regulatory network modelling

Many different approaches have been developed to model and simulate gene regulatory networks. We proposed the following categories for gene regulatory network models: network parts lists, network topology models, network control logic models, and dynamic models. Here we will describe some examples for each of these categories. We will study the topology of gene regulatory networks in yeast in more detail, comparing a direct network derived from transcription factor binding data and an indirect network derived from genome-wide expression data in mutants. Regarding the network dynamics we briefly describe discrete and continuous approaches to network modelling, then describe a hybrid model called Finite State Linear Model and demonstrate that some simple network dynamics can be simulated in this model

Single-cell variability in multicellular organisms

While gene expression noise in single-celled organisms is well understood, it is less so in the context of tissues. Here the authors show that coupling between cells in tissues can increase or decrease cell-to-cell variability depending on the level of noise intrinsic to the regulatory networks

The effects of reminiscence on psychological well-being in older adults: a meta-analysis.

This paper presents the results of a meta-analysis to assess the effectiveness of reminiscence on psychological well-being across different target groups and treatment modalities. Fifteen controlled outcome studies were included. An overall effect size of 0.54 was found, indicating a moderate influence of reminiscence on life-satisfaction and emotional well-being in older adults. Life-review was found to have significantly greater effect on psychological well-being than simple reminiscence. In addition, reminiscence had significantly greater effect on community-dwelling adults than adults living in nursing homes or residential care. Other characteristics of participants or interventions were not found to moderate effects. It is concluded that reminiscence in general, but especially life review, are potentially effective methods for the enhancement of psychological well-being in older adults. However, a replication of effectiveness studies of the well-defined protocols is now warranted. © 2007 Taylor & Francis