Simulating antigenic drift and shift in influenza A

Computational models of the immune system and pathogenic agents have several applications, such as theory testing and validation, or as a complement to first stages of drug trials. One possible application is the prediction of the lethality of new Influenza A strains, which are constantly created due to antigenic drift and shift. Here, we present an agent-based model of immune-influenza A dynamics, with focus on low level molecular antigen-antibody interactions, in order to study antigenic drift and shift events, and analyze the virulence of emergent strains. At this stage of the investigation, results are presented and discussed from a qualitative point of view against recent and generally recognized immunology and influenza literature

Neurocognitive Informatics Manifesto.

Informatics studies all aspects of the structure of natural and artificial information systems. Theoretical and abstract approaches to information have made great advances, but human information processing is still unmatched in many areas, including information management, representation and understanding. Neurocognitive informatics is a new, emerging field that should help to improve the matching of artificial and natural systems, and inspire better computational algorithms to solve problems that are still beyond the reach of machines. In this position paper examples of neurocognitive inspirations and promising directions in this area are given

Parallel pair-wise interaction for multi-agent immune systems modelling

Agent Based Modelling (ABM), is an approach for modelling dynamic systems and studying complex and emergent behaviour. ABM approach is a very common technique in biological domain due to high demand for a large scale analysis tool to collect and interpret information to solve biological problems. However, simulating large scale cellular level models (i.e. large number of agents/entities) require a high degree of computational power which is achievable through parallel computing methods such as Graphics Processing Units (GPUs). The use of parallel approaches in ABMs is growing rapidly specifically when modelling in continuous space system (particle based). Parallel implementation of particle based simulation within continuum space where agents contain quantities of chemicals/substances is very challenging. Pair-wise interactions are different abstraction to continuous space (particle) models which is commonly used for immune system modelling. This paper describes an approach to parallelising the key component of biological and immune system models (pair-wise interactions) within an ABM model. Our performance results demonstrate the applicability of this method to a broader class of biological systems with the same type of cell interactions and that it can be used as the basis for developing complete immune system models on parallel hardware

Nature inspired computational intelligence for financial contagion modelling

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.Financial contagion refers to a scenario in which small shocks, which initially affect only a few financial institutions or a particular region of the economy, spread to the rest of the financial sector and other countries whose economies were previously healthy. This resembles the “transmission” of a medical disease. Financial contagion happens both at domestic level and international level. At domestic level, usually the failure of a domestic bank or financial intermediary triggers transmission by defaulting on inter-bank liabilities, selling assets in a fire sale, and undermining confidence in similar banks. An example of this phenomenon is the failure of Lehman Brothers and the subsequent turmoil in the US financial markets. International financial contagion happens in both advanced economies and developing economies, and is the transmission of financial crises across financial markets. Within the current globalise financial system, with large volumes of cash flow and cross-regional operations of large banks and hedge funds, financial contagion usually happens simultaneously among both domestic institutions and across countries. There is no conclusive definition of financial contagion, most research papers study contagion by analyzing the change in the variance-covariance matrix during the period of market turmoil. King and Wadhwani (1990) first test the correlations between the US, UK and Japan, during the US stock market crash of 1987. Boyer (1997) finds significant increases in correlation during financial crises, and reinforces a definition of financial contagion as a correlation changing during the crash period. Forbes and Rigobon (2002) give a definition of financial contagion. In their work, the term interdependence is used as the alternative to contagion. They claim that for the period they study, there is no contagion but only interdependence. Interdependence leads to common price movements during periods both of stability and turmoil. In the past two decades, many studies (e.g. Kaminsky et at., 1998; Kaminsky 1999) have developed early warning systems focused on the origins of financial crises rather than on financial contagion. Further authors (e.g. Forbes and Rigobon, 2002; Caporale et al, 2005), on the other hand, have focused on studying contagion or interdependence. In this thesis, an overall mechanism is proposed that simulates characteristics of propagating crisis through contagion. Within that scope, a new co-evolutionary market model is developed, where some of the technical traders change their behaviour during crisis to transform into herd traders making their decisions based on market sentiment rather than underlying strategies or factors. The thesis focuses on the transformation of market interdependence into contagion and on the contagion effects. The author first build a multi-national platform to allow different type of players to trade implementing their own rules and considering information from the domestic and a foreign market. Traders’ strategies and the performance of the simulated domestic market are trained using historical prices on both markets, and optimizing artificial market’s parameters through immune - particle swarm optimization techniques (I-PSO). The author also introduces a mechanism contributing to the transformation of technical into herd traders. A generalized auto-regressive conditional heteroscedasticity - copula (GARCH-copula) is further applied to calculate the tail dependence between the affected market and the origin of the crisis, and that parameter is used in the fitness function for selecting the best solutions within the evolving population of possible model parameters, and therefore in the optimization criteria for contagion simulation. The overall model is also applied in predictive mode, where the author optimize in the pre-crisis period using data from the domestic market and the crisis-origin foreign market, and predict in the crisis period using data from the foreign market and predicting the affected domestic market

Aerospace medicine and Biology: A continuing bibliography with indexes, supplement 177

This bibliography lists 112 reports, articles, and other documents introduced into the NASA scientific and technical information system in January 1978

Can persistent Epstein-Barr virus infection induce Chronic Fatigue Syndrome as a Pavlov reflex of the immune response?

Chronic Fatigue Syndrome is a protracted illness condition (lasting even years) appearing with strong flu symptoms and systemic defiances by the immune system. Here, by means of statistical mechanics techniques, we study the most widely accepted picture for its genesis, namely a persistent acute mononucleosis infection, and we show how such infection may drive the immune system toward an out-of-equilibrium metastable state displaying chronic activation of both humoral and cellular responses (a state of full inflammation without a direct "causes-effect" reason). By exploiting a bridge with a neural scenario, we mirror killer lymphocytes $T_K$ and $B$ cells to neurons and helper lymphocytes $T_{H_1},T_{H_2}$ to synapses, hence showing that the immune system may experience the Pavlov conditional reflex phenomenon: if the exposition to a stimulus (EBV antigens) lasts for too long, strong internal correlations among $B,T_K,T_H$ may develop ultimately resulting in a persistent activation even though the stimulus itself is removed. These outcomes are corroborated by several experimental findings.Comment: 26 pages, 9 figures; to appear in the J. Bio. Dy

Equilibrium statistical mechanics on correlated random graphs

Biological and social networks have recently attracted enormous attention between physicists. Among several, two main aspects may be stressed: A non trivial topology of the graph describing the mutual interactions between agents exists and/or, typically, such interactions are essentially (weighted) imitative. Despite such aspects are widely accepted and empirically confirmed, the schemes currently exploited in order to generate the expected topology are based on a-priori assumptions and in most cases still implement constant intensities for links. Here we propose a simple shift in the definition of patterns in an Hopfield model to convert frustration into dilution: By varying the bias of the pattern distribution, the network topology -which is generated by the reciprocal affinities among agents - crosses various well known regimes (fully connected, linearly diverging connectivity, extreme dilution scenario, no network), coupled with small world properties, which, in this context, are emergent and no longer imposed a-priori. The model is investigated at first focusing on these topological properties of the emergent network, then its thermodynamics is analytically solved (at a replica symmetric level) by extending the double stochastic stability technique, and presented together with its fluctuation theory for a picture of criticality. At least at equilibrium, dilution simply decreases the strength of the coupling felt by the spins, but leaves the paramagnetic/ferromagnetic flavors unchanged. The main difference with respect to previous investigations and a naive picture is that within our approach replicas do not appear: instead of (multi)-overlaps as order parameters, we introduce a class of magnetizations on all the possible sub-graphs belonging to the main one investigated: As a consequence, for these objects a closure for a self-consistent relation is achieved.Comment: 30 pages, 4 figure

Immune systems inspired multi-robot cooperative shepherding

Certain tasks require multiple robots to cooperate in order to solve them. The main problem with multi-robot systems is that they are inherently complex and usually situated in a dynamic environment. Now, biological immune systems possess a natural distributed control and exhibit real-time adaptivity, properties that are required to solve problems in multi-robot systems. In this thesis, biological immune systems and their response to external elements to maintain an organism's health state are researched. The objective of this research is to propose immune-inspired approaches to cooperation, to establish an adaptive cooperation algorithm, and to determine the refinements that can be applied in relation to cooperation. Two immune-inspired models that are based on the immune network theory are proposed, namely the Immune Network T-cell-regulated---with Memory (INT-M) and the Immune Network T-cell-regulated---Cross-Reactive (INT-X) models. The INT-M model is further studied where the results have suggested that the model is feasible and suitable to be used, especially in the multi-robot cooperative shepherding domain. The Collecting task in the RoboShepherd scenario and the application of the INT-M algorithm for multi-robot cooperation are discussed. This scenario provides a highly dynamic and complex situation that has wide applicability in real-world problems. The underlying 'mechanism of cooperation' in the immune inspired model (INT-M) is verified to be adaptive in this chosen scenario. Several multi-robot cooperative shepherding factors are studied and refinements proposed, notably methods used for Shepherds' Approach, Shepherds' Formation and Steering Points' Distance. This study also recognises the importance of flock identification in relation to cooperative shepherding, and the Connected Components Labelling method to overcome the related problem is presented. Further work is suggested on the proposed INT-X model that was not implemented in this study, since it builds on top of the INT-M algorithm and its refinements. This study can also be extended to include other shepherding behaviours, further investigation of other useful features of biological immune systems, and the application of the proposed models to other cooperative tasks