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Abstract: This paper explores the robustness of phylogenetic methods for detecting variations in branching and blending signals in the archaeological record. Both processes can generate a spatial structure whereby cultural similarity between different sites decays with increasing spatial distance. By generating a series of artificial records through the controlled and parameterised environment of an agent-based simulation, we: a) illustrate the weakness and the strength of different analytical techniques (empirical distogram, Mantel test, Retention Index, and δ-score); b) determine whether they are capable of assessing how spatial isolation determines cultural diversity; and c) establish whether they can detect variations in the nature of horizontal transmission over time. Results suggest that variables other than the spatial range of interaction (e.g. the frequency of fission events, population dynamics, and rates of cultural innovation) have different effects on the output of some phylogenetic analyses. [Copyright &y& Elsevier]

This paper presents an agent-based simulation (ABS) and cellular automata (CA) coupled model to simulate the spatial evolution of the population of China over the past 2000 years. In the model, agents are used to simulate individuals who live in a geographic environment represented by the CA. The choice to migrate is influenced by climate change, potential agricultural productivity change, and waves of mass migrations. Using the simulation, we can observe the spatial evolution of the population, as well as the shift of the population center of gravity, and we can analyze the driving forces of these changing spatial patterns. [ABSTRACT FROM AUTHOR]

Abstract: Antigen recognition by T cells is a key event in the adaptive immune response. T cells scan the surface of antigen-presenting cells (APCs) or target cells for specific peptides bound to MHC molecules. In the physiological setting, a typical APC presents tens of thousands of diverse endogenous self-derived peptides complexed to MHC (pMHC complexes). When ‘foreign’ peptides are presented, they constitute a small fraction of the total surface peptide repertoire. As T cells seem to be capable of discerning minute amounts of ‘foreign’ peptides among a complex background of self-peptides, endogenous peptides are generally assumed to play no role in recognition. However, recent results suggest that these background peptides may alter the sensitivity of T cells to foreign peptides. Current experimental limitations preclude analysis of peptide mixtures approaching physiological complexity, making it difficult to further address the role of complex background peptides. In this paper, we present a computational model to test how complex, varied peptide populations on an APC could potentially modulate a T cell''s ability to detect the presence of small numbers of agonist peptides among a diverse population. We use the model to investigate the notion that under physiological conditions, T cell recognition of foreign peptides is context dependent, that is, T cells process signals gathered from all pMHC interactions, not just from a few agonist peptides while ignoring all others. [Copyright &y& Elsevier]