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

incaRNAfbinv : a web server for the fragment-based design of RNA sequences

International audienceIn recent years, new methods for computational RNA design have been developed and applied to various problems in synthetic biology and nanotechnology. Lately, there is considerable interest in incorporating essential biological information when solving the inverse RNA folding problem. Correspondingly, RNAfbinv aims at including biologically meaningful constraints and is the only program to-date that performs a fragment-based design of RNA sequences. In doing so it allows the design of sequences that do not necessarily exactly fold into the target, as long as the overall coarse-grained tree graph shape is preserved. Augmented by the weighted sampling algorithm of incaRNAtion, our web server called incaRNAfbinv implements the method devised in RNAfbinv and offers an interactive environment for the inverse folding of RNA using a fragment-based design approach. It takes as input: a target RNA secondary structure; optional sequence and motif constraints; optional target minimum free energy, neutrality, and GC content. In addition to the design of synthetic regulatory sequences, it can be used as a pre-processing step for the detection of novel natural occurring RNAs. The two complementary methodologies RNAfbinv and incaRNAtion are merged together and fully implemented in our web server incaRNAfbinv, available at http://www.cs.bgu. ac.il/incaRNAfbinv

Design of RNAs: comparing programs for inverse RNA folding.

International audienceComputational programs for predicting RNA sequences with desired folding properties have been extensively developed and expanded in the past several years. Given a secondary structure, these programs aim to predict sequences that fold into a target minimum free energy secondary structure, while considering various constraints. This procedure is called inverse RNA folding. Inverse RNA folding has been traditionally used to design optimized RNAs with favorable properties, an application that is expected to grow considerably in the future in light of advances in the expanding new fields of synthetic biology and RNA nanostructures. Moreover, it was recently demonstrated that inverse RNA folding can successfully be used as a valuable preprocessing step in computational detection of novel noncoding RNAs. This review describes the most popular freeware programs that have been developed for such purposes, starting from RNAinverse that was devised when formulating the inverse RNA folding problem. The most recently published ones that consider RNA secondary structure as input are antaRNA, RNAiFold and incaRNAfbinv, each having different features that could be beneficial to specific biological problems in practice. The various programs also use distinct approaches, ranging from ant colony optimization to constraint programming, in addition to adaptive walk, simulated annealing and Boltzmann sampling. This review compares between the various programs and provides a simple description of the various possibilities that would benefit practitioners in selecting the most suitable program. It is geared for specific tasks requiring RNA design based on input secondary structure, with an outlook toward the future of RNA design programs

Leveraging Social Context for Searching Social Media

The ability to utilize and benefit from today’s explosion of social media sites depends on providing tools that allow users to productively participate. In order to participate, users must be able to find resources (both people and information) that they find valuable. Here, we argue that in order to do this effectively, we should make use of a user’s “social context”. A user’s social context includes both their personal social context (their friends and the communities to which they belong) and their community social context (their role and identity in different communities)

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

HnRNP L and L-like cooperate in multiple-exon regulation of CD45 alternative splicing

CD45 encodes a trans-membrane protein-tyrosine phosphatase expressed in diverse cells of the immune system. By combinatorial use of three variable exons 4–6, isoforms are generated that differ in their extracellular domain, thereby modulating phosphatase activity and immune response. Alternative splicing of these CD45 exons involves two heterogeneous ribonucleoproteins, hnRNP L and its cell-type specific paralog hnRNP L-like (LL). To address the complex combinatorial splicing of exons 4–6, we investigated hnRNP L/LL protein expression in human B-cells in relation to CD45 splicing patterns, applying RNA-Seq. In addition, mutational and RNA-binding analyses were carried out in HeLa cells. We conclude that hnRNP LL functions as the major CD45 splicing repressor, with two CA elements in exon 6 as its primary target. In exon 4, one element is targeted by both hnRNP L and LL. In contrast, exon 5 was never repressed on its own and only co-regulated with exons 4 and 6. Stable L/LL interaction requires CD45 RNA, specifically exons 4 and 6. We propose a novel model of combinatorial alternative splicing: HnRNP L and LL cooperate on the CD45 pre-mRNA, bridging exons 4 and 6 and looping out exon 5, thereby achieving full repression of the three variable exons

The Dynamics Of Social Contagion

Social contagion is a subset of contagion which includes all social phenomena that can and do spread via social networks. The notion of how something becomes popular is very relevant to the concept of social contagion. Rumors, fads, and opinions can spread through social networks like wildfire, "infecting" individuals until they become the norm. This thesis investigates the dynamics of social contagion, employing a combination of formal analysis, simulation, and empirical data mining approaches to examine the processes whereby social contagion spreads throughout social networks. I introduce the concept of critical mass for a subclass of social contagion called complex contagion. This concept builds on earlier work to describe the nonlinear dynamics whereby most socially contagious phenomena infect very few people while a few become overwhelmingly popular. I also investigate socially contagious phenomena that arise when rational agents act under conditions of local information. Finally, I examine how my analytic work applies to a large dataset of empirical social contagion and draw implications for further research in the area

Salience vs. commitment: dynamics of political hashtags in Russian Twitter

Social media sites like Twitter enable users to engage in the spread of contagious phenomena: everything from information and rumors to social movements and virally marketed products. In particular, Twitter has been observed to function as a platform for political discourse, allowing political movements to spread their message and engage supporters, and also as a platform for information diffusion, allowing everyone from mass media to citizens to reach a wide audience with a critical piece of news. Previous work1 suggests that different contagious phenomena will display distinct propagation dynamics, and in particular that news will spread differently through a population than other phenomena. We leverage this theory to construct a system for classifying contagious phenomena based on the properties of their propagation dynamics, by combining temporal and network features. Our system, applicable to phenomena in any social media platform or genre, is applied to a dataset of news-related and political hashtags diffusing through the population of Russian Twitter users. Our results show that news-related hashtags have a distinctive pattern of propagation across the spectrum of Russian Twitter users. In contrast, we find that political hashtags display a number of different dynamic signatures corresponding to different politically active sub-communities. Analysis using ‘chronotopes’ sharpens these findings and reveals an important propagation pattern we call ‘resonant salience.