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

Spectra of "Real-World" Graphs: Beyond the Semi-Circle Law

Many natural and social systems develop complex networks, that are usually modelled as random graphs. The eigenvalue spectrum of these graphs provides information about their structural properties. While the semi-circle law is known to describe the spectral density of uncorrelated random graphs, much less is known about the eigenvalues of real-world graphs, describing such complex systems as the Internet, metabolic pathways, networks of power stations, scientific collaborations or movie actors, which are inherently correlated and usually very sparse. An important limitation in addressing the spectra of these systems is that the numerical determination of the spectra for systems with more than a few thousand nodes is prohibitively time and memory consuming. Making use of recent advances in algorithms for spectral characterization, here we develop new methods to determine the eigenvalues of networks comparable in size to real systems, obtaining several surprising results on the spectra of adjacency matrices corresponding to models of real-world graphs. We find that when the number of links grows as the number of nodes, the spectral density of uncorrelated random graphs does not converge to the semi-circle law. Furthermore, the spectral densities of real-world graphs have specific features depending on the details of the corresponding models. In particular, scale-free graphs develop a triangle-like spectral density with a power law tail, while small-world graphs have a complex spectral density function consisting of several sharp peaks. These and further results indicate that the spectra of correlated graphs represent a practical tool for graph classification and can provide useful insight into the relevant structural properties of real networks.Comment: 14 pages, 9 figures (corrected typos, added references) accepted for Phys. Rev.

Freezing by Heating in a Driven Mesoscopic System

We investigate a simple model corresponding to particles driven in opposite directions and interacting via a repulsive potential. The particles move off-lattice on a periodic strip and are subject to random forces as well. We show that this model - which can be considered as a continuum version of some driven diffusive systems - exhibits a paradoxial, new kind of transition called here ``freezing by heating''. One interesting feature of this transition is that a crystallized state with a higher total energy is obtained from a fluid state by increasing the amount of fluctuations.Comment: For related work see http://www.theo2.physik.uni-stuttgart.de/helbing.html and http://angel.elte.hu/~vicsek

Low fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAP) diet improves symptoms in adults suffering from irritable bowel syndrome (IBS) compared to standard IBS diet: A meta-analysis of clinical studies

BACKGROUND: Irritable bowel syndrome (IBS) and functional digestive tract disorders, e.g. functional bloating, carbohydrate maldigestion and intolerances, are very common disorders frequently causing significant symptoms that challenge health care systems. A low Fermentable Oligosaccharides, Disaccharides, Monosaccharides and Polyols (FODMAP) diet is one of the possible therapeutic approaches for decreasing abdominal symptoms and improving quality of life. OBJECTIVES: We aimed to meta-analyze data on the therapeutic effect of a low-FODMAP diet on symptoms of IBS and quality of life and compare its effectiveness to a regular, standard IBS diet with high FODMAP content, using a common scoring system, the IBS Symptom Severity Score (IBS-SSS). METHODS: A systematic literature search was conducted in PubMed, EMBASE and the Cochrane Library as well as in the references in a recent meta-analysis. Adult patients diagnosed with IBS according to the Rome II, Rome III, Rome IV or NICE criteria were included in the analysis. STATISTICAL METHODS: Mean differences with 95% confidence intervals were calculated from studies that contained means, standard deviation (SD) or mean differences and SD of differences and p-values. A random effect model was used because of the heterogeneity (Q test (chi2) and I2 indicator). A p-value of less than 0.05 was chosen to indicate a significant difference. RESULTS: The literature search yielded 902 publications, but only 10 were eligible for our meta-analysis. Both regular and low-FODMAP diets proved to be effective in IBS, but post-diet IBS-SSS values were significantly lower (p = 0.002) in the low-FODMAP group. The low-FODMAP diet showed a correlation with the improvement of general symptoms (by IBS-SSS) in patients with IBS. CONCLUSIONS: This meta-analysis provides high-grade evidence of an improved general symptom score among patients with irritable bowel syndrome who have maintained a low-FODMAP diet compared to those on a traditional IBS diet, therefore showing its superiority to regular IBS dietary therapy. These data suggest that a low-FODMAP diet with dietitian control can be a candidate for first-line therapeutic modality in IBS. Because of a lack of data, well-planned randomized controlled studies are needed to ascertain the correlation between improvement of separate key IBS symptoms and the effect of a low-FODMAP diet

Recurrent acute pancreatitis prevention by the elimination of alcohol and cigarette smoking (REAPPEAR): protocol of a randomised controlled trial and a cohort study

Background/objectives Acute recurrent pancreatitis (ARP) due to alcohol and/or tobacco abuse is a preventable disease which lowers quality of life and can lead to chronic pancreatitis. The REAPPEAR study aims to investigate whether a combined patient education and cessation programme for smoking and alcohol prevents ARP. Methods and analysis The REAPPEAR study consists of an international multicentre randomised controlled trial (REAPPEAR-T) testing the efficacy of a cessation programme on alcohol and smoking and a prospective cohort study (REAPPEAR-C) assessing the effects of change in alcohol consumption and smoking (irrespective of intervention). Daily smoker patients hospitalised with alcohol-induced acute pancreatitis (AP) will be enrolled. All patients will receive a standard intervention priorly to encourage alcohol and smoking cessation. Participants will be subjected to laboratory testing, measurement of blood pressure and body mass index and will provide blood, hair and urine samples for later biomarker analysis. Addiction, motivation to change, socioeconomic status and quality of life will be evaluated with questionnaires. In the trial, patients will be randomised either to the cessation programme with 3-monthly visits or to the control group with annual visits. Participants of the cessation programme will receive a brief intervention at every visit with direct feedback on their alcohol consumption based on laboratory results. The primary endpoint will be the composite of 2-year all-cause recurrence rate of AP and/or 2-year all-cause mortality. The cost-effectiveness of the cessation programme will be evaluated. An estimated 182 participants will be enrolled per group to the REAPPEAR-T with further enrolment to the cohort

Mitochondrial dysfunction and autism: Comprehensive genetic analyses of children with autism and mtDNA deletion

Additional file 1: Table S1. Investigated genes responsible for mtDNA maintenance (intergenomic NGS panel)

Het fenomeen delta : landschap van Nico de Jonge = The phenomenon Delta : a Nico de Jonge's landscape

Nico M. De Jonge, emeritus hoogleraar landschapsarchitectuur aan de Landbouwuniversiteit Wageningen, heeft een belangrijk deel van zijn leven gewijd aan de vormgeving van landschappen in de Rijn-Scheldedelta. Het boek gaat over het unieke landschap van de delta, op de grens van land en water, van cultuur en natuur, van bestaan en verbeelding. Er wordt ingegaan op ontwikkelingen en planning aan Nederlandse en Vlaamse kant van de delta, er wordt een vergelijking gemaakt tussen deltagebieden over de wereld, en De Jonges visie op de ontwikkeling van de landschapsarchitectuur komt aan bod