Evolutionary Prisoner's Dilemma on heterogeneous Newman-Watts small-world network

We focus on the heterogeneity of social networks and its role to the emergence of prevailing cooperation and sustaining cooperators. The social networks are representative of the interaction relationships between players and their encounters in each round of games. We study an evolutionary Prisoner's Dilemma game on a variant of Watts-Strogatz small-world network, whose heterogeneity can be tuned by a parameter. It is found that optimal cooperation level exists at some intermediate topological heterogeneity for different temptations to defect. Moreover, neither the most heterogeneous case nor the most homogeneous one would favor the cooperators. At intermediate heterogeneity in degree sequences, cooperators could resist the invasion of defectors for large temptation to defect.Comment: Updated versio

Discovery of active proteins directly from combinatorial randomized protein libraries without display, purification or sequencing:identification of novel zinc finger proteins.

We have successfully linked protein library screening directly with the identification of active proteins, without the need for individual purification, display technologies or physical linkage between the protein and its encoding sequence. By using 'MAX' randomization we have rapidly constructed 60 overlapping gene libraries that encode zinc finger proteins, randomized variously at the three principal DNA-contacting residues. Expression and screening of the libraries against five possible target DNA sequences generated data points covering a potential 40,000 individual interactions. Comparative analysis of the resulting data enabled direct identification of active proteins. Accuracy of this library analysis methodology was confirmed by both in vitro and in vivo analyses of identified proteins to yield novel zinc finger proteins that bind to their target sequences with high affinity, as indicated by low nanomolar apparent dissociation constants

Drinfeld Twists and Symmetric Bethe Vectors of Supersymmetric Fermion Models

We construct the Drinfeld twists (factorizing $F$-matrices) of the $gl(m|n)$-invariant fermion model. Completely symmetric representation of the pseudo-particle creation operators of the model are obtained in the basis provided by the $F$-matrix (the $F$-basis). We resolve the hierarchy of the nested Bethe vectors in the $F$-basis for the $gl(m|n)$ supersymmetric model.Comment: Latex File, 24 pages, no figure, some misprints are correcte

Fluorescent microplate-based analysis of protein-DNA interactions II:immobilized DNA

A simple protein-DNA interaction analysis has been developed using both a high-affinity/high-specificity zinc finger protein and a low-specificity zinc finger protein with nonspecific DNA binding capability. The latter protein is designed to mimic background binding by proteins generated in randomized or shuffled gene libraries. In essence, DNA is immobilized onto the surface of microplate wells via streptavidin capture, and green fluorescent protein (GFP)-labeled protein is added in solution as part of a crude cell lysate or protein mixture. After incubation and washing, bound protein is detected in a standard microplate reader. The minimum sensitivity of the assay is approximately 0.4 nM protein. The assay format is ideally suited to investigate the interactions of DNA binding proteins from within crude cell extracts and/or mixtures of proteins that may be encountered in protein libraries generated by codon randomization or gene shuffling

High Resolution He-like Argon And Sulfur Spectra From The PSI ECRIT

We present new results on the X-ray spectroscopy of multicharged argon, sulfur and chlorine obtained with the Electron Cyclotron Resonance Ion Trap (ECRIT) in operation at the Paul Scherrer Institut (Villigen, Switzerland). We used a Johann-type Bragg spectrometer with a spherically-bent crystal, with an energy resolution of about 0.4 eV. The ECRIT itself is of a hybrid type, with a superconducting split coil magnet, special iron inserts which provides the mirror field, and a permanent magnetic hexapole. The high frequency was provided by a 6.4 GHz microwave emitter. We obtained high intensity X-ray spectra of multicharged F-like to He-like argon, sulfur and chlorine with one 1s hole. In particular, we observed the 1s2s^{3}S_1 \to 1s^2^{1}S_0 M1 and 1s2p^{3}P_2 \to 1s^2^{1}S_0 M2 transitions in He-like argon, sulfur and chlorine with unprecedented statistics and resolution. The energies of the observed lines are being determined with good accuracy using the He-like M1 line as a reference

Fluorescent microplate-based analysis of protein-DNA interactions I:immobilized protein

A simple protein-DNA interaction analysis has been developed using a high-affinity/high-specificity zinc finger protein. In essence, purified protein samples are immobilized directly onto the surface of microplate wells, and fluorescently labeled DNA is added in solution. After incubation and washing, bound DNA is detected in a standard microplate reader. The minimum sensitivity of the assay is approximately 0.2 nM DNA. Since the detection of bound DNA is noninvasive and the protein-DNA interaction is not disrupted during detection, iterative readings may be taken from the same well, after successive alterations in interaction conditions, if required. In this respect, the assay may therefore be considered real time and permits appropriate interaction conditions to be determined quantitatively. The assay format is ideally suited to investigate the interactions of purified unlabeled DNA binding proteins in a high-throughput format

On the complexity of color-avoiding site and bond percolation

The mathematical analysis of robustness and error-tolerance of complex networks has been in the center of research interest. On the other hand, little work has been done when the attack-tolerance of the vertices or edges are not independent but certain classes of vertices or edges share a mutual vulnerability. In this study, we consider a graph and we assign colors to the vertices or edges, where the color-classes correspond to the shared vulnerabilities. An important problem is to find robustly connected vertex sets: nodes that remain connected to each other by paths providing any type of error (i.e. erasing any vertices or edges of the given color). This is also known as color-avoiding percolation. In this paper, we study various possible modeling approaches of shared vulnerabilities, we analyze the computational complexity of finding the robustly (color-avoiding) connected components. We find that the presented approaches differ significantly regarding their complexity.Comment: 14 page

Regulation of immunocompetence by different androgen metabolites in a blenny with alternative reproductive tactics

In Parablennius parvicornis, small reproductive males with relatively low expression of secondary sexual characters (M morphotype) parasite on the parental investment of the larger nest-holder males which have fully developed secondary sexual characters (M1 morphotype). In comparison with M1 males, M males have relatively low levels of androgens while having high blood cell percentages of lymphocytes and antigen responsiveness. Here we test the hypothesis that androgens are a causal factor for these differences in immunocompetence between morphotypes. After drawing an initial blood sample, males received a silastic implant containing either oil only (C), or oil with testosterone (T) or 11-ketotestosterone (KT). Males were re-caught 2 weeks later for drawing of the final blood sample. KT but not T induced the development of secondary sexual characters in M males. M males treated with KT showed lower swimming activity than the males treated with T or C implants, suggesting that KT also mediates behavioral changes in M males. As expected, blood cell percentages of lymphocytes, but not of granulocytes, were higher in M males than in M1 males. Overall, lymphocyte percentages increased in the C group which might have been a response to the surgery/treatment. In concordance with the hypothesis, lymphocyte percentages were suppressed in males treated with T in comparison with controls. However, no significant change was found in KT-treated males. This suggests that androgens modulate central, morphological and immunological traits by partly independent androgen mechanisms in P. parvicornis

Comment on "Critique of q-entropy for thermal statistics" by M. Nauenberg

It was recently published by M. Nauenberg [1] a quite long list of objections about the physical validity for thermal statistics of the theory sometimes referred to in the literature as {\it nonextensive statistical mechanics}. This generalization of Boltzmann-Gibbs (BG) statistical mechanics is based on the following expression for the entropy: S_q= k\frac{1- \sum_{i=1}^Wp_i^q}{q-1} (q \in {\cal R}; S_1=S_{BG} \equiv -k\sum_{i=1}^W p_i \ln p_i) . The author of [1] already presented orally the essence of his arguments in 1993 during a scientific meeting in Buenos Aires. I am replying now simultaneously to the just cited paper, as well as to the 1993 objections (essentially, the violation of "fundamental thermodynamic concepts", as stated in the Abstract of [1]).Comment: 7 pages including 2 figures. This is a reply to M. Nauenberg, Phys. Rev. E 67, 036114 (2003

Molecular systematics of the genus Artibeus (Chiroptera

a b s t r a c t A molecular phylogeny of the genus Artibeus using 19 of the 20 recognized species, many with samples from a broad geographic range, is presented. The analysis shows a clear distinction between the two subgenera (or genera), the 'large' Artibeus and the 'small' Dermanura, in both mitochondrial and nuclear genes. The placement and status of A. concolor remains inconclusive and is presented as the third subgenus Koopmania. The phylogenies and divergence time estimates show a marked influence of the Andes in the formation of the subgenera and the main lineages inside each subgenus. Nuclear genes showed a highly incomplete lineage sorting among species inside subgenera Artibeus and Dermanura. Indeed, shared alleles were also found between Artibeus and Koopmania, which are presumed to have split apart during the Miocene, showing that great care should be taken in using these markers. Cytochrome-b gene divergences and monophyly analyses suggest that A. lituratus and A. intermedius are indeed conspecifics. These analyses also suggested the existence of at least four 'new' species revealing a significant cryptic diversity inside the genus