101,406 research outputs found

    A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland

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    Phylogenetic clustering approaches can elucidate HIV transmission dynamics. Comparisons across countries are essential for evaluating public health policies. Here, we used a standardised approach to compare the UK HIV Drug Resistance Database and the Swiss HIV Cohort Study while maintaining data-protection requirements. Clusters were identified in subtype A1, B and C pol phylogenies. We generated degree distributions for each risk group and compared distributions between countries using Kolmogorov-Smirnov (KS) tests, Degree Distribution Quantification and Comparison (DDQC) and bootstrapping. We used logistic regression to predict cluster membership based on country, sampling date, risk group, ethnicity and sex. We analysed >8,000 Swiss and >30,000 UK subtype B sequences. At 4.5% genetic distance, the UK was more clustered and MSM and heterosexual degree distributions differed significantly by the KS test. The KS test is sensitive to variation in network scale, and jackknifing the UK MSM dataset to the size of the Swiss dataset removed the difference. Only heterosexuals varied based on the DDQC, due to UK male heterosexuals who clustered exclusively with MSM. Their removal eliminated this difference. In conclusion, the UK and Swiss HIV epidemics have similar underlying dynamics and observed differences in clustering are mainly due to different population sizes

    Quantification and Comparison of Degree Distributions in Complex Networks

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    The degree distribution is an important characteristic of complex networks. In many applications, quantification of degree distribution in the form of a fixed-length feature vector is a necessary step. On the other hand, we often need to compare the degree distribution of two given networks and extract the amount of similarity between the two distributions. In this paper, we propose a novel method for quantification of the degree distributions in complex networks. Based on this quantification method,a new distance function is also proposed for degree distributions, which captures the differences in the overall structure of the two given distributions. The proposed method is able to effectively compare networks even with different scales, and outperforms the state of the art methods considerably, with respect to the accuracy of the distance function

    Feature Extraction from Degree Distribution for Comparison and Analysis of Complex Networks

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    The degree distribution is an important characteristic of complex networks. In many data analysis applications, the networks should be represented as fixed-length feature vectors and therefore the feature extraction from the degree distribution is a necessary step. Moreover, many applications need a similarity function for comparison of complex networks based on their degree distributions. Such a similarity measure has many applications including classification and clustering of network instances, evaluation of network sampling methods, anomaly detection, and study of epidemic dynamics. The existing methods are unable to effectively capture the similarity of degree distributions, particularly when the corresponding networks have different sizes. Based on our observations about the structure of the degree distributions in networks over time, we propose a feature extraction and a similarity function for the degree distributions in complex networks. We propose to calculate the feature values based on the mean and standard deviation of the node degrees in order to decrease the effect of the network size on the extracted features. The proposed method is evaluated using different artificial and real network datasets, and it outperforms the state of the art methods with respect to the accuracy of the distance function and the effectiveness of the extracted features.Comment: arXiv admin note: substantial text overlap with arXiv:1307.362

    The Small World of Osteocytes: Connectomics of the Lacuno-Canalicular Network in Bone

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    Osteocytes and their cell processes reside in a large, interconnected network of voids pervading the mineralized bone matrix of most vertebrates. This osteocyte lacuno-canalicular network (OLCN) is believed to play important roles in mechanosensing, mineral homeostasis, and for the mechanical properties of bone. While the extracellular matrix structure of bone is extensively studied on ultrastructural and macroscopic scales, there is a lack of quantitative knowledge on how the cellular network is organized. Using a recently introduced imaging and quantification approach, we analyze the OLCN in different bone types from mouse and sheep that exhibit different degrees of structural organization not only of the cell network but also of the fibrous matrix deposited by the cells. We define a number of robust, quantitative measures that are derived from the theory of complex networks. These measures enable us to gain insights into how efficient the network is organized with regard to intercellular transport and communication. Our analysis shows that the cell network in regularly organized, slow-growing bone tissue from sheep is less connected, but more efficiently organized compared to irregular and fast-growing bone tissue from mice. On the level of statistical topological properties (edges per node, edge length and degree distribution), both network types are indistinguishable, highlighting that despite pronounced differences at the tissue level, the topological architecture of the osteocyte canalicular network at the subcellular level may be independent of species and bone type. Our results suggest a universal mechanism underlying the self-organization of individual cells into a large, interconnected network during bone formation and mineralization

    Quantifying the consistency of scientific databases

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    Science is a social process with far-reaching impact on our modern society. In the recent years, for the first time we are able to scientifically study the science itself. This is enabled by massive amounts of data on scientific publications that is increasingly becoming available. The data is contained in several databases such as Web of Science or PubMed, maintained by various public and private entities. Unfortunately, these databases are not always consistent, which considerably hinders this study. Relying on the powerful framework of complex networks, we conduct a systematic analysis of the consistency among six major scientific databases. We found that identifying a single "best" database is far from easy. Nevertheless, our results indicate appreciable differences in mutual consistency of different databases, which we interpret as recipes for future bibliometric studies.Comment: 20 pages, 5 figures, 4 table

    The multi-layer network nature of systemic risk and its implications for the costs of financial crises

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    The inability to see and quantify systemic financial risk comes at an immense social cost. Systemic risk in the financial system arises to a large extent as a consequence of the interconnectedness of its institutions, which are linked through networks of different types of financial contracts, such as credit, derivatives, foreign exchange and securities. The interplay of the various exposure networks can be represented as layers in a financial multi-layer network. In this work we quantify the daily contributions to systemic risk from four layers of the Mexican banking system from 2007-2013. We show that focusing on a single layer underestimates the total systemic risk by up to 90%. By assigning systemic risk levels to individual banks we study the systemic risk profile of the Mexican banking system on all market layers. This profile can be used to quantify systemic risk on a national level in terms of nation-wide expected systemic losses. We show that market-based systemic risk indicators systematically underestimate expected systemic losses. We find that expected systemic losses are up to a factor four higher now than before the financial crisis of 2007-2008. We find that systemic risk contributions of individual transactions can be up to a factor of thousand higher than the corresponding credit risk, which creates huge risks for the public. We find an intriguing non-linear effect whereby the sum of systemic risk of all layers underestimates the total risk. The method presented here is the first objective data driven quantification of systemic risk on national scales that reveal its true levels.Comment: 15 pages, 6 figure
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