Fast filtering and animation of large dynamic networks

Detecting and visualizing what are the most relevant changes in an evolving network is an open challenge in several domains. We present a fast algorithm that filters subsets of the strongest nodes and edges representing an evolving weighted graph and visualize it by either creating a movie, or by streaming it to an interactive network visualization tool. The algorithm is an approximation of exponential sliding time-window that scales linearly with the number of interactions. We compare the algorithm against rectangular and exponential sliding time-window methods. Our network filtering algorithm: i) captures persistent trends in the structure of dynamic weighted networks, ii) smoothens transitions between the snapshots of dynamic network, and iii) uses limited memory and processor time. The algorithm is publicly available as open-source software.Comment: 6 figures, 2 table

Distinguishing Topical and Social Groups Based on Common Identity and Bond Theory

Social groups play a crucial role in social media platforms because they form the basis for user participation and engagement. Groups are created explicitly by members of the community, but also form organically as members interact. Due to their importance, they have been studied widely (e.g., community detection, evolution, activity, etc.). One of the key questions for understanding how such groups evolve is whether there are different types of groups and how they differ. In Sociology, theories have been proposed to help explain how such groups form. In particular, the common identity and common bond theory states that people join groups based on identity (i.e., interest in the topics discussed) or bond attachment (i.e., social relationships). The theory has been applied qualitatively to small groups to classify them as either topical or social. We use the identity and bond theory to define a set of features to classify groups into those two categories. Using a dataset from Flickr, we extract user-defined groups and automatically-detected groups, obtained from a community detection algorithm. We discuss the process of manual labeling of groups into social or topical and present results of predicting the group label based on the defined features. We directly validate the predictions of the theory showing that the metrics are able to forecast the group type with high accuracy. In addition, we present a comparison between declared and detected groups along topicality and sociality dimensions.Comment: 10 pages, 6 figures, 2 table

Complex networks approach to modeling online social systems. The emergence of computational social science

This thesis is devoted to quantitative description, analysis, and modeling of complex social systems in the form of online social networks. Statistical patterns of the systems under study are unveiled and interpreted using concepts and methods of network science, social network analysis, and data mining. A long-term promise of this research is that predicting the behavior of complex techno-social systems will be possible in a way similar to contemporary weather forecasting, using statistical inference and computational modeling based on the advancements in understanding and knowledge of techno-social systems. Although the subject of this study are humans, as opposed to atoms or molecules in statistical physics, the availability of extremely large datasets on human behavior permits the use of tools and techniques of statistical physics. This dissertation deals with large datasets from online social networks, measures statistical patterns of social behavior, and develops quantitative methods, models, and metrics for complex techno-social systemsLa presente tesis está dedicada a la descripción, análisis y modelado cuantitativo de sistemas complejos sociales en forma de redes sociales en internet. Mediante el uso de métodos y conceptos provenientes de ciencia de redes, análisis de redes sociales y minería de datos se descubren diferentes patrones estadísticos de los sistemas estudiados. Uno de los objetivos a largo plazo de esta línea de investigación consiste en hacer posible la predicción del comportamiento de sistemas complejos tecnológico-sociales, de un modo similar a la predicción meteorológica, usando inferencia estadística y modelado computacional basado en avances en el conocimiento de los sistemas tecnológico-sociales. A pesar de que el objeto del presente estudio son seres humanos, en lugar de los átomos o moléculas estudiados tradicionalmente en la física estadística, la disponibilidad de grandes bases de datos sobre comportamiento humano hace posible el uso de técnicas y métodos de física estadística. En el presente trabajo se utilizan grandes bases de datos provenientes de redes sociales en internet, se miden patrones estadísticos de comportamiento social, y se desarrollan métodos cuantitativos, modelos y métricas para el estudio de sistemas complejos tecnológico-sociales

A mutant Escherichia coli that attaches peptidoglycan to lipopolysaccharide and displays cell wall on its surface

The lipopolysaccharide (LPS) forms the surface-exposed leaflet of the outer membrane (OM) of Gram-negative bacteria, an organelle that shields the underlying peptidoglycan (PG) cell wall. Both LPS and PG are essential cell envelope components that are synthesized independently and assembled by dedicated transenvelope multiprotein complexes. We have identified a point-mutation in the gene for O-antigen ligase (WaaL) in Escherichia coli that causes LPS to be modified with PG subunits, intersecting these two pathways. Synthesis of the PG-modified LPS (LPS*) requires ready access to the small PG precursor pool but does not weaken cell wall integrity, challenging models of precursor sequestration at PG assembly machinery. LPS* is efficiently transported to the cell surface without impairing OM function. Because LPS* contains the canonical vancomycin binding site, these surface-exposed molecules confer increased vancomycin-resistance by functioning as molecular decoys that titrate the antibiotic away from its intracellular target. This unexpected LPS glycosylation fuses two potent pathogen-associated molecular patterns (PAMPs). DOI: http://dx.doi.org/10.7554/eLife.05334.00

Heterogeneity shapes groups growth in social online communities

Many complex systems are characterized by broad distributions capturing, for example, the size of firms, the population of cities or the degree distribution of complex networks. Typically this feature is explained by means of a preferential growth mechanism. Although heterogeneity is expected to play a role in the evolution it is usually not considered in the modeling probably due to a lack of empirical evidence on how it is distributed. We characterize the intrinsic heterogeneity of groups in an online community and then show that together with a simple linear growth and an inhomogeneous birth rate it explains the broad distribution of group members.Comment: 5 pages, 3 figure panel

Opinion Dynamics of Learning Agents: Does Seeking Consensus Lead to Disagreement?

We study opinion dynamics in a population of interacting adaptive agents voting on a set of complex multidimensional issues. We consider agents which can classify issues into for or against. The agents arrive at the opinions about each issue in question using an adaptive algorithm. Adaptation comes from learning and the information for the learning process comes from interacting with other neighboring agents and trying to change the internal state in order to concur with their opinions. The change in the internal state is driven by the information contained in the issue and in the opinion of the other agent. We present results in a simple yet rich context where each agent uses a Boolean Perceptron to state its opinion. If there is no internal clock, so the update occurs with asynchronously exchanged information among pairs of agents, then the typical case, if the number of issues is kept small, is the evolution into a society thorn by the emergence of factions with extreme opposite beliefs. This occurs even when seeking consensus with agents with opposite opinions. The curious result is that it is learning from those that hold the same opinions that drives the emergence of factions. This results follows from the fact that factions are prevented by not learning at all from those agents that hold the same opinion. If the number of issues is large, the dynamics becomes trapped and the society does not evolve into factions and a distribution of moderate opinions is observed. We also study the less realistic, but technically simpler synchronous case showing that global consensus is a fixed point. However, the approach to this consensus is glassy in the limit of large societies if agents adapt even in the case of agreement.Comment: 16 pages, 10 figures, revised versio

Dynamics in online social networks

An increasing number of today's social interactions occurs using online social media as communication channels. Some online social networks have become extremely popular in the last decade. They differ among themselves in the character of the service they provide to online users. For instance, Facebook can be seen mainly as a platform for keeping in touch with close friends and relatives, Twitter is used to propagate and receive news, LinkedIn facilitates the maintenance of professional contacts, Flickr gathers amateurs and professionals of photography, etc. Albeit different, all these online platforms share an ingredient that pervades all their applications. There exists an underlying social network that allows their users to keep in touch with each other and helps to engage them in common activities or interactions leading to a better fulfillment of the service's purposes. This is the reason why these platforms share a good number of functionalities, e.g., personal communication channels, broadcasted status updates, easy one-step information sharing, news feeds exposing broadcasted content, etc. As a result, online social networks are an interesting field to study an online social behavior that seems to be generic among the different online services. Since at the bottom of these services lays a network of declared relations and the basic interactions in these platforms tend to be pairwise, a natural methodology for studying these systems is provided by network science. In this chapter we describe some of the results of research studies on the structure, dynamics and social activity in online social networks. We present them in the interdisciplinary context of network science, sociological studies and computer science.Comment: 17 pages, 4 figures, book chapte

Trapped lipopolysaccharide and LptD intermediates reveal lipopolysaccharide translocation steps across the Escherichia coli outer membrane

Lipopolysaccharide (LPS) is a main component of the outer membrane of Gram-negative bacteria, which is essential for the vitality of most Gram-negative bacteria and plays a critical role for drug resistance. LptD/E complex forms a N-terminal LPS transport slide, a hydrophobic intramembrane hole and the hydrophilic channel of the barrel, for LPS transport, lipid A insertion and core oligosaccharide and O-antigen polysaccharide translocation, respectively. However, there is no direct evidence to confirm that LptD/E transports LPS from the periplasm to the external leaflet of the outer membrane. By replacing LptD residues with an unnatural amino acid p-benzoyl-L-phenyalanine (pBPA) and UV-photo-cross-linking in E.coli, the translocon and LPS intermediates were obtained at the N-terminal domain, the intramembrane hole, the lumenal gate, the lumen of LptD channel, and the extracellular loop 1 and 4, providing the first direct evidence and “snapshots” to reveal LPS translocation steps across the outer membrane

Effects of Research Paper Promotion via ArXiv and X

In the evolving landscape of scientific publishing, it is important to understand the drivers of high-impact research, to equip scientists with actionable strategies to enhance the reach of their work, and to understand trends in the use of modern scientific publishing tools to inform their further development. Here, we study trends in the use of early preprint publications and revisions on ArXiv and the use of X (formerly Twitter) for promotion of such papers in computer science and physics. We find that early submissions to ArXiv and promotion on X have soared in recent years. Estimating the effect that the use of each of these modern affordances has on the number of citations of scientific publications, we find that peer-reviewed conference papers in computer science that are submitted early to ArXiv gain on average $21.1 \pm 17.4$ more citations, revised on ArXiv gain $18.4 \pm 17.6$ more citations, and promoted on X gain $44.4 \pm 8$ more citations in the first 5 years from an initial publication. In contrast, journal articles in physics experience comparatively lower boosts in citation counts, with increases of $3.9 \pm 1.1$, $4.3 \pm 0.9$, and $6.9 \pm 3.5$ citations respectively for the same interventions. Our results show that promoting one's work on ArXiv or X has a large impact on the number of citations, as well as the number of influential citations computed by Semantic Scholar, and thereby on the career of researchers. These effects are present also for publications in physics, but they are relatively smaller. The larger relative effect sizes, effects of promotion accumulating over time, and elevated unpredictability of the number of citations in computer science than in physics suggest a greater role of world-of-mouth spreading in computer science than in physics