In-depth analysis of the Naming Game dynamics: the homogeneous mixing case

Language emergence and evolution has recently gained growing attention through multi-agent models and mathematical frameworks to study their behavior. Here we investigate further the Naming Game, a model able to account for the emergence of a shared vocabulary of form-meaning associations through social/cultural learning. Due to the simplicity of both the structure of the agents and their interaction rules, the dynamics of this model can be analyzed in great detail using numerical simulations and analytical arguments. This paper first reviews some existing results and then presents a new overall understanding.Comment: 30 pages, 19 figures (few in reduced definition). In press in IJMP

Sharp transition towards shared vocabularies in multi-agent systems

What processes can explain how very large populations are able to converge on the use of a particular word or grammatical construction without global coordination? Answering this question helps to understand why new language constructs usually propagate along an S-shaped curve with a rather sudden transition towards global agreement. It also helps to analyze and design new technologies that support or orchestrate self-organizing communication systems, such as recent social tagging systems for the web. The article introduces and studies a microscopic model of communicating autonomous agents performing language games without any central control. We show that the system undergoes a disorder/order transition, going trough a sharp symmetry breaking process to reach a shared set of conventions. Before the transition, the system builds up non-trivial scale-invariant correlations, for instance in the distribution of competing synonyms, which display a Zipf-like law. These correlations make the system ready for the transition towards shared conventions, which, observed on the time-scale of collective behaviors, becomes sharper and sharper with system size. This surprising result not only explains why human language can scale up to very large populations but also suggests ways to optimize artificial semiotic dynamics.Comment: 12 pages, 4 figure

1928-29: Abilene Christian College Bible Lectures - Full Text

INTRODUCTION It has been the custom of Abilene Christian College for several years to hold an annual “Lectureship” the last week in February. This is a time of gathering of brethren from all over the state and adjoining states. It is a time of a great spiritual feast. It affords an opportunity for brethren to meet and talk over the work of the Lord. It also enables us to hear again great men of God whose voices have sounded the Word of the Lord in the days of the past in great meetings. In order that those who are not permitted to hear the lectures may enjoy them it has been the custom of Abilene Christian College to publish the lectures in a book at the end of each two years. We feel that these wonderful messages from some of the greatest minds of the church ought to be preserved that they may do good even after the lips of the speakers have become silent. It is with a prayer that great good may come that this volume of lectures of 1928 and 1929 is sent forth. We regret that some of the lectures could not be included in the book. Several of the brethren neglected to send in their manuscripts; some other manuscripts were destroyed by fire, and the brethren did not replace them. Most\u27 of the lectures are in the book. BATSELL BAXTER. DELIVERED IN THE AUDITORIUM OF ABILENE CHRISTIAN COLLEGE ABILENE, TEXAS FEBRUARY 1928-1929 FIRM FOUNDATION PUBLISHING HOUSE 104-106-108 E. 9th Street Austin, Texas

UniPROBE: an online database of protein binding microarray data on protein–DNA interactions

The UniPROBE (Universal PBM Resource for Oligonucleotide Binding Evaluation) database hosts data generated by universal protein binding microarray (PBM) technology on the in vitro DNA-binding specificities of proteins. This initial release of the UniPROBE database provides a centralized resource for accessing comprehensive PBM data on the preferences of proteins for all possible sequence variants (‘words’) of length k (‘k-mers’), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. In total, the database hosts DNA-binding data for over 175 nonredundant proteins from a diverse collection of organisms, including the prokaryote Vibrio harveyi, the eukaryotic malarial parasite Plasmodium falciparum, the parasitic Apicomplexan Cryptosporidium parvum, the yeast Saccharomyces cerevisiae, the worm Caenorhabditis elegans, mouse and human. Current web tools include a text-based search, a function for assessing motif similarity between user-entered data and database PWMs, and a function for locating putative binding sites along user-entered nucleotide sequences. The UniPROBE database is available at http://thebrain.bwh.harvard.edu/uniprobe/

Monolingual Biases in Simulations of Cultural Transmission

Recent research suggests that the evolution of language is affected by the inductive biases of its learners. I suggest that there is an implicit assumption that one of these biases is to expect a single linguistic system in the input. Given the prevalence of bilingual cultures, this may not be a valid abstraction. This is illustrated by demonstrating that the ‘minimal naming game’ model, in which a shared lexicon evolves in a population of agents, includes an implicit mutual exclusivity bias. Since recent research suggests that children raised in bilingual cultures do not exhibit mutual exclusivity, the individual learning algorithm of the agents is not as abstract as it appears to be. A modification of this model demonstrates that communicative success can be achieved without mutual exclusivity. It is concluded that complex cultural phenomena, such as bilingualism, do not necessarily result from complex individual learning mechanisms. Rather, the cultural process itself can bring about this complexity

A variational method based on weighted graph states

In a recent article [Phys. Rev. Lett. 97 (2006), 107206], we have presented a class of states which is suitable as a variational set to find ground states in spin systems of arbitrary spatial dimension and with long-range entanglement. Here, we continue the exposition of our technique, extend from spin 1/2 to higher spins and use the boson Hubbard model as a non-trivial example to demonstrate our scheme.Comment: 36 pages, 13 figure

Bistability in Apoptosis by Receptor Clustering

Apoptosis is a highly regulated cell death mechanism involved in many physiological processes. A key component of extrinsically activated apoptosis is the death receptor Fas, which, on binding to its cognate ligand FasL, oligomerize to form the death-inducing signaling complex. Motivated by recent experimental data, we propose a mathematical model of death ligand-receptor dynamics where FasL acts as a clustering agent for Fas, which form locally stable signaling platforms through proximity-induced receptor interactions. Significantly, the model exhibits hysteresis, providing an upstream mechanism for bistability and robustness. At low receptor concentrations, the bistability is contingent on the trimerism of FasL. Moreover, irreversible bistability, representing a committed cell death decision, emerges at high concentrations, which may be achieved through receptor pre-association or localization onto membrane lipid rafts. Thus, our model provides a novel theory for these observed biological phenomena within the unified context of bistability. Importantly, as Fas interactions initiate the extrinsic apoptotic pathway, our model also suggests a mechanism by which cells may function as bistable life/death switches independently of any such dynamics in their downstream components. Our results highlight the role of death receptors in deciding cell fate and add to the signal processing capabilities attributed to receptor clustering.Comment: Accepted by PLoS Comput Bio

Recombination rate and selection strength in HIV intra-patient evolution

The evolutionary dynamics of HIV during the chronic phase of infection is driven by the host immune response and by selective pressures exerted through drug treatment. To understand and model the evolution of HIV quantitatively, the parameters governing genetic diversification and the strength of selection need to be known. While mutation rates can be measured in single replication cycles, the relevant effective recombination rate depends on the probability of coinfection of a cell with more than one virus and can only be inferred from population data. However, most population genetic estimators for recombination rates assume absence of selection and are hence of limited applicability to HIV, since positive and purifying selection are important in HIV evolution. Here, we estimate the rate of recombination and the distribution of selection coefficients from time-resolved sequence data tracking the evolution of HIV within single patients. By examining temporal changes in the genetic composition of the population, we estimate the effective recombination to be r=1.4e-5 recombinations per site and generation. Furthermore, we provide evidence that selection coefficients of at least 15% of the observed non-synonymous polymorphisms exceed 0.8% per generation. These results provide a basis for a more detailed understanding of the evolution of HIV. A particularly interesting case is evolution in response to drug treatment, where recombination can facilitate the rapid acquisition of multiple resistance mutations. With the methods developed here, more precise and more detailed studies will be possible, as soon as data with higher time resolution and greater sample sizes is available.Comment: to appear in PLoS Computational Biolog

West Nile virus: characterization and diagnostic applications of monoclonal antibodies

<p>Abstract</p> <p>Background</p> <p>Diagnosis of West Nile virus (WNV) infections is often difficult due to the extensive antigenic cross-reactivity among flaviviruses, especially in geographic regions where two or more of these viruses are present causing sequential infections. The purpose of this study was to characterize a panel of monoclonal antibodies (MAbs) produced against WNV to verify their applicability in WNV diagnosis and in mapping epitope targets of neutralizing MAbs.</p> <p>Methods</p> <p>Six MAbs were produced and characterized by isotyping, virus-neutralization, western blotting and MAb-epitope competition. The MAb reactivity against various WNVs belonging to lineage 1 and 2 and other related flaviviruses was also evaluated. The molecular basis of epitopes recognized by neutralizing MAbs was defined through the selection and sequencing of MAb escape mutants. Competitive binding assays between MAbs and experimental equine and chicken sera were designed to identify specific MAb reaction to epitopes with high immunogenicity.</p> <p>Results</p> <p>All MAbs showed stronger reactivity with all WNVs tested and good competition for antigen binding in ELISA tests with WNV-positive equine and chicken sera. Four MAbs (3B2, 3D6, 4D3, 1C3) resulted specific for WNV, while two MAbs (2A8, 4G9) showed cross-reaction with Usutu virus. Three MAbs (3B2, 3D6, 4D3) showed neutralizing activity. Sequence analysis of 3B2 and 3D6 escape mutants showed an amino acid change at E307 (Lys → Glu) in the E protein gene, whereas 4D3 variants identified mutations encoding amino acid changed at E276 (Ser → Ile) or E278 (Thr → Ile). 3B2 and 3D6 mapped to a region on the lateral surface of domain III of E protein, which is known to be a specific and strong neutralizing epitope for WNV, while MAb 4D3 recognized a novel specific neutralizing epitope on domain II of E protein that has not previously been described with WNV MAbs.</p> <p>Conclusions</p> <p>MAbs generated in this study can be applied to various analytical methods for virological and serological WNV diagnosis. A novel WNV-specific and neutralizing MAb (4D3) directed against the unknown epitope on domain II of E protein can be useful to better understand the role of E protein epitopes involved in the mechanism of WNV neutralization.</p