Exploring Russian Cyberspace: Digitally-Mediated Collective Action and the Networked Public Sphere

This paper summarizes the major findings of a three-year research project to investigate the Internet's impact on Russian politics, media and society. We employed multiple methods to study online activity: the mapping and study of the structure, communities and content of the blogosphere; an analogous mapping and study of Twitter; content analysis of different media sources using automated and human-based evaluation approaches; and a survey of bloggers; augmented by infrastructure mapping, interviews and background research. We find the emergence of a vibrant and diverse networked public sphere that constitutes an independent alternative to the more tightly controlled offline media and political space, as well as the growing use of digital platforms in social mobilization and civic action. Despite various indirect efforts to shape cyberspace into an environment that is friendlier towards the government, we find that the Russian Internet remains generally open and free, although the current degree of Internet freedom is in no way a prediction of the future of this contested space

Quasiclassical description of transport through superconducting contacts

We present a theoretical study of transport properties through superconducting contacts based on a new formulation of boundary conditions that mimics interfaces for the quasiclassical theory of superconductivity. These boundary conditions are based on a description of an interface in terms of a simple Hamiltonian. We show how this Hamiltonian description is incorporated into quasiclassical theory via a T-matrix equation by integrating out irrelevant energy scales right at the onset. The resulting boundary conditions reproduce results obtained by conventional quasiclassical boundary conditions, or by boundary conditions based on the scattering approach. This formalism is well suited for the analysis of magnetically active interfaces as well as for calculating time-dependent properties such as the current-voltage characteristics or as current fluctuations in junctions with arbitrary transmission and bias voltage. This approach is illustrated with the calculation of Josephson currents through a variety of superconducting junctions ranging from conventional to d-wave superconductors, and to the analysis of supercurrent through a ferromagnetic nanoparticle. The calculation of the current-voltage characteristics and of noise is applied to the case of a contact between two d-wave superconductors. In particular, we discuss the use of shot noise for the measurement of charge transferred in a multiple Andreev reflection in d-wave superconductors

The stealth episome: suppression of gene expression on the excised genomic island PPHGI-1 from Pseudomonas syringae pv. phaseolicola

Pseudomonas syringae pv. phaseolicola is the causative agent of halo blight in the common bean, Phaseolus vulgaris. P. syringae pv. phaseolicola race 4 strain 1302A contains the avirulence gene avrPphB (syn. hopAR1), which resides on PPHGI-1, a 106 kb genomic island. Loss of PPHGI-1 from P. syringae pv. phaseolicola 1302A following exposure to the hypersensitive resistance response (HR) leads to the evolution of strains with altered virulence. Here we have used fluorescent protein reporter systems to gain insight into the mobility of PPHGI-1. Confocal imaging of dual-labelled P. syringae pv. phaseolicola 1302A strain, F532 (dsRFP in chromosome and eGFP in PPHGI-1), revealed loss of PPHGI-1::eGFP encoded fluorescence during plant infection and when grown in vitro on extracted leaf apoplastic fluids. Fluorescence-activated cell sorting (FACS) of fluorescent and non-fluorescent PPHGI-1::eGFP F532 populations showed that cells lost fluorescence not only when the GI was deleted, but also when it had excised and was present as a circular episome. In addition to reduced expression of eGFP, quantitative PCR on sub-populations separated by FACS showed that transcription of other genes on PPHGI-1 (avrPphB and xerC) was also greatly reduced in F532 cells harbouring the excised PPHGI-1::eGFP episome. Our results show how virulence determinants located on mobile pathogenicity islands may be hidden from detection by host surveillance systems through the suppression of gene expression in the episomal state

Explorando o Ciberespaço Russo: Ação Coletiva Digitalmente Mediada e a Esfera Pública Interconectada

Propósito – Este artigo sintetiza os principais achados de um projeto de pesquisa de três anos para investigar o impacto da Internet sobre a política, a mídia e a sociedade russa. Metodologia/abordagem/design – Empregamos múltiplos métodos para estudar atividades online: o mapeamento e estudo da estrutura, das comunidades e do conteúdo da blogosfera; um análogo mapeamento e estudo do Twitter; a análise de conteúdo de diferentes fontes midiáticas, utilizando tanto abordagens automatizadas quanto abordagens baseadas em avaliação humana; e uma enquete com blogueiros; métodos esses expandidos por mapeamento de infraestrutura, por entrevistas e por investigações de contexto. Resultados – Constatamos a emergência de uma vibrante e diversa esfera pública interconectada, que constitui uma alternativa independente ao mais rigidamente controlado espaço midiático e político offline, e verificamos o uso crescente de plataformas digitais na mobilização social e na ação cívica. Implicações práticas – Apesar da existência de vários esforços indiretos para conformar o ciberespaço como um ambiente mais amigável ao governo, constatamos que a Internet russa permanece, em geral, aberta e livre, embora o atual grau de liberdade na Internet de forma alguma possa representar previsão acerca do futuro desse espaço contestado

Spin current in ferromagnet/insulator/superconductor junctions

A theory of spin polarized tunneling spectroscopy based on a scattering theory is given for tunneling junctions between ferromagnets and d-wave superconductors. The spin filtering effect of an exchange field in the insulator is also treated. We clarify that the properties of the Andreev reflection are largely modified due to a presence of an exchange field in the ferromagnets, and consequently the Andreev reflected quasiparticle shows an evanescent-wave behavior depending on the injection angle of the quasiparticle. Conductance formulas for the spin current as well as the charge current are given as a function of the applied voltage and the spin-polarization in the ferromagnet for arbitrary barrier heights. It is shown that the surface bound states do not contribute to the spin current and that the zero-bias conductance peak expected for a d-wave superconductor splits into two peaks under the influence of the exchange interaction in the insulator.Comment: 14 pages, 11 figure

Anisotropy of magnetothermal conductivity in Sr2RuO4

The dependence of in-plane and interplane thermal conductivities of Sr2RuO4 on temperature, as well as magnetic field strength and orientation, is reported. We found no notable anisotropy in the thermal conductivity for the magnetic field rotation parallel to the conducting plane in the whole range of experimental temperatures and fields, except in the vicinity of the upper critical field Hc2, where the anisotropy of the Hc2 itself plays a dominant role. This finding imposes strong constraints on the possible models of superconductivity in Sr2RuO4 and supports the existence of a superconducting gap with a line of nodes running orthogonal to the Fermi surface cylinder.Comment: published in Phys. Rev. Lett. 4pages, 4 eps figures, LaTe

Threat-sensitive anti-predator defence in precocial wader, the northern lapwing Vanellus vanellus

Birds exhibit various forms of anti-predator behaviours to avoid reproductive failure, with mobbing—observation, approach and usually harassment of a predator—being one of the most commonly observed. Here, we investigate patterns of temporal variation in the mobbing response exhibited by a precocial species, the northern lapwing (Vanellus vanellus). We test whether brood age and self-reliance, or the perceived risk posed by various predators, affect mobbing response of lapwings. We quantified aggressive interactions between lapwings and their natural avian predators and used generalized additive models to test how timing and predator species identity are related to the mobbing response of lapwings. Lapwings diversified mobbing response within the breeding season and depending on predator species. Raven Corvus corax, hooded crow Corvus cornix and harriers evoked the strongest response, while common buzzard Buteo buteo, white stork Ciconia ciconia, black-headed gull Chroicocephalus ridibundus and rook Corvus frugilegus were less frequently attacked. Lapwings increased their mobbing response against raven, common buzzard, white stork and rook throughout the breeding season, while defence against hooded crow, harriers and black-headed gull did not exhibit clear temporal patterns. Mobbing behaviour of lapwings apparently constitutes a flexible anti-predator strategy. The anti-predator response depends on predator species, which may suggest that lapwings distinguish between predator types and match mobbing response to the perceived hazard at different stages of the breeding cycle. We conclude that a single species may exhibit various patterns of temporal variation in anti-predator defence, which may correspond with various hypotheses derived from parental investment theory

Association of IGF-I gene polymorphisms with milk yield and body size in Chinese dairy goats

The association of IGF-I gene polymorphisms with certain traits in 708 individuals of two Chinese dairy-goat breeds (Guanzhong and Xinong Saanen) was investigated. Polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and DNA sequencing methods were employed in screening for genetic variation. Two novel mutations were detected in the 5'-flanking region and in intron 4 of IGF-I gene, viz., g.1617 G > A and g.5752 G > C (accession D26119.2), respectively. The associations of the g.1617 G > A mutation with milk yield and the body size were not significant (p > 0.05). However, in the case of g.5752 G > C, Xinong Saanen dairy goats with the CG genotype presented longer bodies (p < 0.05). Chest circumference (p < 0.05) was larger in Guanzhong goats with the GG genotype. In Xinong Saanen dairy goats with the CC genotype, milk yields were significantly higher during the first and second lactations (p < 0.05). Hence, the g.5752 G > C mutation could facilitate association analysis and serve as a genetic marker for Chinese dairy-goat breeding and genetics

Average and extreme multi-atom Van der Waals interactions: Strong coupling of multi-atom Van der Waals interactions with covalent bonding

<p>Abstract</p> <p>Background</p> <p>The prediction of ligand binding or protein structure requires very accurate force field potentials – even small errors in force field potentials can make a 'wrong' structure (from the billions possible) more stable than the single, 'correct' one. However, despite huge efforts to optimize them, currently-used all-atom force fields are still not able, in a vast majority of cases, even to keep a protein molecule in its native conformation in the course of molecular dynamics simulations or to bring an approximate, homology-based model of protein structure closer to its native conformation.</p> <p>Results</p> <p>A strict analysis shows that a specific coupling of multi-atom Van der Waals interactions with covalent bonding can, in extreme cases, increase (or decrease) the interaction energy by about 20–40% at certain angles between the direction of interaction and the covalent bond. It is also shown that on average multi-body effects decrease the total Van der Waals energy in proportion to the square root of the electronic component of dielectric permittivity corresponding to dipole-dipole interactions at small distances, where Van der Waals interactions take place.</p> <p>Conclusion</p> <p>The study shows that currently-ignored multi-atom Van der Waals interactions can, in certain instances, lead to significant energy effects, comparable to those caused by the replacement of atoms (for instance, C by N) in conventional pairwise Van der Waals interactions.</p

The influence of the accessory genome on bacterial pathogen evolution

Bacterial pathogens exhibit significant variation in their genomic content of virulence factors. This reflects the abundance of strategies pathogens evolved to infect host organisms by suppressing host immunity. Molecular arms-races have been a strong driving force for the evolution of pathogenicity, with pathogens often encoding overlapping or redundant functions, such as type III protein secretion effectors and hosts encoding ever more sophisticated immune systems. The pathogens’ frequent exposure to other microbes, either in their host or in the environment, provides opportunities for the acquisition or interchange of mobile genetic elements. These DNA elements accessorise the core genome and can play major roles in shaping genome structure and altering the complement of virulence factors. Here, we review the different mobile genetic elements focusing on the more recent discoveries and highlighting their role in shaping bacterial pathogen evolution