Uncovering the overlapping community structure of complex networks in nature and society

Many complex systems in nature and society can be described in terms of networks capturing the intricate web of connections among the units they are made of. A key question is how to interpret the global organization of such networks as the coexistence of their structural subunits (communities) associated with more highly interconnected parts. Identifying these a priori unknown building blocks (such as functionally related proteins, industrial sectors and groups of people) is crucial to the understanding of the structural and functional properties of networks. The existing deterministic methods used for large networks find separated communities, whereas most of the actual networks are made of highly overlapping cohesive groups of nodes. Here we introduce an approach to analysing the main statistical features of the interwoven sets of overlapping communities that makes a step towards uncovering the modular structure of complex systems. After defining a set of new characteristic quantities for the statistics of communities, we apply an efficient technique for exploring overlapping communities on a large scale. We find that overlaps are significant, and the distributions we introduce reveal universal features of networks. Our studies of collaboration, word-association and protein interaction graphs show that the web of communities has non-trivial correlations and specific scaling properties.Comment: The free academic research software, CFinder, used for the publication is available at the website of the publication: http://angel.elte.hu/clusterin

The inner core hemispheric boundary near 180°W

The inner core (IC) east–west hemispheric dichotomy is widely recognized, but the reported position of the hemispheric boundary varies among studies due to uneven sampling coverage and the data analyzed. This study investigates the sharpness of the western hemispheric boundary (WHB) near 180°W by analyzing differential time residuals of PKiKP–PKPdf and PKP(bc–df) for PKPdf phases that sample 155°E–130°W in various azimuthal directions. Using PKiKP–PKPdf observations, the WHB is located at 175°E–180°W in the southern hemisphere, based mainly on the lateral isotropy–anisotropy transition. However, based on the lateral isotropic velocity contrast and this isotropy–anisotropy transition between the two hemispheres, its location is 170–160°W in the northern hemisphere. These findings indicate that the WHB is sharp and exhibits a latitudinal dependence with a 10°–20° kink, as well as 1.75% anisotropy in the uppermost IC across the 180–155°W range of the western hemisphere. As suggested by PKP(bc–df), the WHB could remain at 160°W at depth. The isotropic velocity contrast near the WHB (160°W) between the eastern and western hemispheres is lower than previous estimates using PKPdf phases sampling the bulk part of each hemisphere

Estimated HIV Incidence in the United States, 2006–2009

Background The estimated number of new HIV infections in the United States reflects the leading edge of the epidemic. Previously, CDC estimated HIV incidence in the United States in 2006 as 56,300 (95% CI: 48,200–64,500). We updated the 2006 estimate and calculated incidence for 2007–2009 using improved methodology. Methodology We estimated incidence using incidence surveillance data from 16 states and 2 cities and a modification of our previously described stratified extrapolation method based on a sample survey approach with multiple imputation, stratification, and extrapolation to account for missing data and heterogeneity of HIV testing behavior among population groups. Principal Findings Estimated HIV incidence among persons aged 13 years and older was 48,600 (95% CI: 42,400–54,700) in 2006, 56,000 (95% CI: 49,100–62,900) in 2007, 47,800 (95% CI: 41,800–53,800) in 2008 and 48,100 (95% CI: 42,200–54,000) in 2009. From 2006 to 2009 incidence did not change significantly overall or among specific race/ethnicity or risk groups. However, there was a 21% (95% CI:1.9%–39.8%; p = 0.017) increase in incidence for people aged 13–29 years, driven by a 34% (95% CI: 8.4%–60.4%) increase in young men who have sex with men (MSM). There was a 48% increase among young black/African American MSM (12.3%–83.0%; p<0.001). Among people aged 13–29, only MSM experienced significant increases in incidence, and among 13–29 year-old MSM, incidence increased significantly among young, black/African American MSM. In 2009, MSM accounted for 61% of new infections, heterosexual contact 27%, injection drug use (IDU) 9%, and MSM/IDU 3%. Conclusions/Significance Overall, HIV incidence in the United States was relatively stable 2006–2009; however, among young MSM, particularly black/African American MSM, incidence increased. HIV continues to be a major public health burden, disproportionately affecting several populations in the United States, especially MSM and racial and ethnic minorities. Expanded, improved, and targeted prevention is necessary to reduce HIV incidence

Source Characteristics of the 2016 Meinong (ML 6.6) Taiwan Earthquake Revealed from Dense Seismic Arrays: Double Sources and Pulse-like Velocity Ground Motion

The 5 February 2016, Meinong, Taiwan, earthquake brought extensive damage to nearby cities with significant pulse‐like velocity ground motions. In addition to the spatial slip distribution determination using filtered strong‐motion data, we show that, with the advantage of the densely distributed seismic network as a seismic array, we can project the earthquake sources (asperities) directly using nearly unfiltered data, which is crucial to the understanding of the generation of the pulse‐like velocity ground motions. We recognize that the moderate but damaging ML 6.6 Meinong earthquake was a composite of an Mw 5.5 foreshock and an Mw 6.18 mainshock with a 1.8–5.0 s time delay. The foreshock occurred at the hypocenter reported by the official agency, followed by the mainshock with a centroid located at 12.3 km to the north‐northwest of the hypocenter and at a depth of 15 km. This foreshock–mainshock composition is not distinguishable in the finite‐fault inversion because it filtered the seismic data to low frequencies. Our results show that the pulse‐like velocity ground motions are mainly attributed to the source of mainshock with its directivity and site effects, resulting in the disastrous damages in the city of Tainan. Although finite‐fault inversion using filtered seismic data for spatial slip distribution on the fault has been a classic procedure in understanding earthquake rupture processes, using a dense seismic network as a seismic array for unfiltered records helps us delineate the earthquake sources directly and provide more delicate information for future understanding of earthquake source complexity

Lifshitz/Schr\"odinger D-p-branes and dynamical exponents

We extend our earlier study of special double limits of `boosted' $AdS_5$ black hole solutions to include all black D$p$-branes of type II strings. We find that Lifshitz solutions can be obtained in generality, with varied dynamical exponents, by employing these limits. We then study such double limits for `boosted' D$p$-brane bubble solutions and find that the resulting non-relativistic solutions instead describe Schr\"odinger like spacetimes, having varied dynamical exponents. We get a simple map between these Lifshitz & Schr\"odinger solutions and a relationship between two types of dynamical exponents. We also discuss about the singularities of the Lifshitz solutions and an intriguing thermodynamic duality.Comment: 20 pages; 3 figures; v3: similar to JHE

Set optimization - a rather short introduction

Recent developments in set optimization are surveyed and extended including various set relations as well as fundamental constructions of a convex analysis for set- and vector-valued functions, and duality for set optimization problems. Extensive sections with bibliographical comments summarize the state of the art. Applications to vector optimization and financial risk measures are discussed along with algorithmic approaches to set optimization problems

Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-seq and ESTs

The reference annotations made for a genome sequence provide the framework for all subsequent analyses of the genome. Correct annotation is particularly important when interpreting the results of RNA-seq experiments where short sequence reads are mapped against the genome and assigned to genes according to the annotation. Inconsistencies in annotations between the reference and the experimental system can lead to incorrect interpretation of the effect on RNA expression of an experimental treatment or mutation in the system under study. Until recently, the genome-wide annotation of 3-prime untranslated regions received less attention than coding regions and the delineation of intron/exon boundaries. In this paper, data produced for samples in Human, Chicken and A. thaliana by the novel single-molecule, strand-specific, Direct RNA Sequencing technology from Helicos Biosciences which locates 3-prime polyadenylation sites to within +/- 2 nt, were combined with archival EST and RNA-Seq data. Nine examples are illustrated where this combination of data allowed: (1) gene and 3-prime UTR re-annotation (including extension of one 3-prime UTR by 5.9 kb); (2) disentangling of gene expression in complex regions; (3) clearer interpretation of small RNA expression and (4) identification of novel genes. While the specific examples displayed here may become obsolete as genome sequences and their annotations are refined, the principles laid out in this paper will be of general use both to those annotating genomes and those seeking to interpret existing publically available annotations in the context of their own experimental dataComment: 44 pages, 9 figure

White matter changes in microstructure associated with a maladaptive response to stress in rats

In today's society, every individual is subjected to stressful stimuli with different intensities and duration. This exposure can be a key trigger in several mental illnesses greatly affecting one's quality of life. Yet not all subjects respond equally to the same stimulus and some are able to better adapt to them delaying the onset of its negative consequences. The neural specificities of this adaptation can be essential to understand the true dynamics of stress as well as to design new approaches to reduce its consequences. In the current work, we employed ex vivo high field diffusion magnetic resonance imaging (MRI) to uncover the differences in white matter properties in the entire brain between Fisher 344 (F344) and Sprague-Dawley (SD) rats, known to present different responses to stress, and to examine the effects of a 2-week repeated inescapable stress paradigm. We applied a tract-based spatial statistics (TBSS) analysis approach to a total of 25 animals. After exposure to stress, SD rats were found to have lower values of corticosterone when compared with F344 rats. Overall, stress was found to lead to an overall increase in fractional anisotropy (FA), on top of a reduction in mean and radial diffusivity (MD and RD) in several white matter bundles of the brain. No effect of strain on the white matter diffusion properties was observed. The strain-by-stress interaction revealed an effect on SD rats in MD, RD and axial diffusivity (AD), with lower diffusion metric levels on stressed animals. These effects were localized on the left side of the brain on the external capsule, corpus callosum, deep cerebral white matter, anterior commissure, endopiriform nucleus, dorsal hippocampus and amygdala fibers. The results possibly reveal an adaptation of the SD strain to the stressful stimuli through synaptic and structural plasticity processes, possibly reflecting learning processes.We thank Neurospin (high field MRI center CEA Saclay) for providing its support for MRI acquisition. JB was supported by grants from Fondation pour la Recherche Médicale (FRM) and Groupe Pasteur Mutualité (GPM). This work was supported by a grant from ANR (SIGMA). This work was performed on a platform of France Life Imaging (FLI) network partly funded by the grant ANR-11-INBS-0006. This work and RM were supported by a fellowship of the project FCT-ANR/NEU-OSD/0258/2012 founded by FCT/MEC (www.fct.pt) and by Fundo Europeu de Desenvolvimento Regional (FEDER). AC was supported by a grant from the Fondation NRJ.info:eu-repo/semantics/publishedVersio