278 research outputs found
Universal hierarchical behavior of citation networks
Many of the essential features of the evolution of scientific research are imprinted in the structure of citation networks. Connections in these networks imply information about the transfer of knowledge among papers, or, in other words, edges describe the impact of papers on other publications. This inherent meaning of the edges implies that citation networks can exhibit hierarchical features that are typical of networks based on decision making. In this paper, we investigate the hierarchical structure of citation networks consisting of papers in the same field. We find that the majority of the networks follow a universal trend towards a highly hierarchical state, and the various fields display differences only concerning (i)their phase in life (distance from the 'birth' of a field) or (ii)the characteristic time according to which they are approaching the stationary state. We also show by a simple argument that the alterations in the behavior are related to and can be understood by the degree of specialization corresponding to the fields. Our results suggest that during the accumulation of knowledge in a given field, some papers are gradually becoming relatively more influential than most other papers. © 2014 IOP Publishing Ltd and SISSA Medialab srl
A Systems Biology Interpretation of Array Comparative Genomic Hybridization (aCGH) Data through Phylogenetics
Array Comparative Genomic Hybridization (aCGH) is a rapid screening technique to detect gene deletions and duplications, providing an overview of chromosomal aberrations throughout the entire genome of a tumor, without the need for cell culturing. However, the heterogeneity of aCGH data obfuscates existing methods of data analysis. Analysis of aCGH data from a systems biology perspective or in the context of total aberrations is largely absent in the published literature. We present here a novel alternative to the functional analysis of aCGH data using the phylogenetic paradigm that is well-suited to high dimensional datasets of heterogeneous nature, but has not been widely adapted to aCGH data. Maximum parsimony phylogenetic analysis sorts out genetic data through the simplest presentation of the data on a cladogram, a graphical evolutionary tree, thus providing a powerful and efficient method for aCGH data analysis. For example, the cladogram models the multiphasic changes in the cancer genome and identifies shared early mutations in the disease progression, providing a simple yet powerful means of aCGH data interpretation. As such, applying maximum parsimony phylogenetic analysis to aCGH results allows for the differentiation between drivers and passenger genes aberrations in cancer specimens. In addition to offering a novel methodology to analyze aCGH results, we present here a crucial software suite that we wrote to carry out the analysis. In a broader context, we wish to underscore that phylogenetic analysis of aCGH data is a non-parametric method that circumvents the pitfalls and frustrations of standard analytical techniques that rely on parametric statistics. Organizing the data in a cladogram as explained in this research article provides insights into the disease common aberrations, as well as the disease subtypes and their shared aberrations (the synapomorphies) of each subtype. Hence, we report the method and make the software suite publicly and freely available at http://software.phylomcs.com so that researchers can test alternative and innovative approaches to the analysis of aCGH data
A universal preconditioner for simulating condensed phase materials.
We introduce a universal sparse preconditioner that accelerates geometry optimisation and saddle point search tasks that are common in the atomic scale simulation of materials. Our preconditioner is based on the neighbourhood structure and we demonstrate the gain in computational efficiency in a wide range of materials that include metals, insulators, and molecular solids. The simple structure of the preconditioner means that the gains can be realised in practice not only when using expensive electronic structure models but also for fast empirical potentials. Even for relatively small systems of a few hundred atoms, we observe speedups of a factor of two or more, and the gain grows with system size. An open source Python implementation within the Atomic Simulation Environment is available, offering interfaces to a wide range of atomistic codes
Effect of correlations on network controllability
A dynamical system is controllable if by imposing appropriate external
signals on a subset of its nodes, it can be driven from any initial state to
any desired state in finite time. Here we study the impact of various network
characteristics on the minimal number of driver nodes required to control a
network. We find that clustering and modularity have no discernible impact, but
the symmetries of the underlying matching problem can produce linear, quadratic
or no dependence on degree correlation coefficients, depending on the nature of
the underlying correlations. The results are supported by numerical simulations
and help narrow the observed gap between the predicted and the observed number
of driver nodes in real networks
Comparing the hierarchy of keywords in on-line news portals
The tagging of on-line content with informative keywords is a widespread
phenomenon from scientific article repositories through blogs to on-line news
portals. In most of the cases, the tags on a given item are free words chosen
by the authors independently. Therefore, relations among keywords in a
collection of news items is unknown. However, in most cases the topics and
concepts described by these keywords are forming a latent hierarchy, with the
more general topics and categories at the top, and more specialised ones at the
bottom. Here we apply a recent, cooccurrence-based tag hierarchy extraction
method to sets of keywords obtained from four different on-line news portals.
The resulting hierarchies show substantial differences not just in the topics
rendered as important (being at the top of the hierarchy) or of less interest
(categorised low in the hierarchy), but also in the underlying network
structure. This reveals discrepancies between the plausible keyword association
frameworks in the studied news portals
Hierarchy measure for complex networks
Nature, technology and society are full of complexity arising from the
intricate web of the interactions among the units of the related systems (e.g.,
proteins, computers, people). Consequently, one of the most successful recent
approaches to capturing the fundamental features of the structure and dynamics
of complex systems has been the investigation of the networks associated with
the above units (nodes) together with their relations (edges). Most complex
systems have an inherently hierarchical organization and, correspondingly, the
networks behind them also exhibit hierarchical features. Indeed, several papers
have been devoted to describing this essential aspect of networks, however,
without resulting in a widely accepted, converging concept concerning the
quantitative characterization of the level of their hierarchy. Here we develop
an approach and propose a quantity (measure) which is simple enough to be
widely applicable, reveals a number of universal features of the organization
of real-world networks and, as we demonstrate, is capable of capturing the
essential features of the structure and the degree of hierarchy in a complex
network. The measure we introduce is based on a generalization of the m-reach
centrality, which we first extend to directed/partially directed graphs. Then,
we define the global reaching centrality (GRC), which is the difference between
the maximum and the average value of the generalized reach centralities over
the network. We investigate the behavior of the GRC considering both a
synthetic model with an adjustable level of hierarchy and real networks.
Results for real networks show that our hierarchy measure is related to the
controllability of the given system. We also propose a visualization procedure
for large complex networks that can be used to obtain an overall qualitative
picture about the nature of their hierarchical structure.Comment: 29 pages, 9 figures, 4 table
Using metadynamics to explore complex free-energy landscapes
Metadynamics is an atomistic simulation technique that allows, within the same framework, acceleration of rare events and estimation of the free energy of complex molecular systems. It is based on iteratively \u2018filling\u2019 the potential energy of the system by a sum of Gaussians centred along the trajectory followed by a suitably chosen set of collective variables (CVs), thereby forcing the system to migrate from one minimum to the next. The power of metadynamics is demonstrated by the large number of extensions and variants that have been developed. The first scope of this Technical Review is to present a critical comparison of these variants, discussing their advantages and disadvantages. The effectiveness of metadynamics, and that of the numerous alternative methods, is strongly influenced by the choice of the CVs. If an important variable is neglected, the resulting estimate of the free energy is unreliable, and predicted transition mechanisms may be qualitatively wrong. The second scope of this Technical Review is to discuss how the CVs should be selected, how to verify whether the chosen CVs are sufficient or redundant, and how to iteratively improve the CVs using machine learning approaches
Effect of lutein and antioxidant dietary supplementation on contrast sensitivity in age-related macular disease:A randomized controlled trial
Objective: The aim of the study is to determine the effect of lutein combined with vitamin and mineral supplementation on contrast sensitivity in people with age-related macular disease (ARMD). Design: A prospective, 9-month, double-masked randomized controlled trial. Setting: Aston University, Birmingham, UK and a UK optometric clinical practice. Subjects: Age-related maculopathy (ARM) and atrophic age-related macular degeneration (AMD) participants were randomized (using a random number generator) to either placebo (n = 10) or active (n=15) groups. Three of the placebo group and two of the active group dropped out. Interventions: The active group supplemented daily with 6 mg lutein combined with vitamins and minerals. The outcome measure was contrast sensitivity (CS) measured using the Pelli-Robson chart, for which the study had 80% power at the 5% significance level to detect a change of 0.3log units. Results: The CS score increased by 0.07 ± 0.07 and decreased by 0.02 ± 0.18 log units for the placebo and active groups, respectively. The difference between these values is not statistically significant (z = 0.903, P = 0.376). Conclusion: The results suggest that 6 mg of lutein supplementation in combination with other antioxidants is not beneficial for this group. Further work is required to establish optimum dosage levels
Video monitoring of neovessel occlusion induced by photodynamic therapy with verteporfin (Visudyne®), in the CAM model
The aim of the present study was to monitor photodynamic angioocclusion with verteporfin in capillaries. Details of this process were recorded under a microscope in real-time using a high-sensitivity video camera. A procedure was developed based on intravenous (i.v.) injection of a light-activated drug, Visudyne®, into the chorioallantoic membrane (CAM) of a 12-day-old chicken embryo. The effect of light activation was probed after 24 h by i.v. injection of a fluorescent dye (FITC dextran), and analysis of its fluorescence distribution. The angioocclusive effect was graded based on the size of the occluded vessels, and these results were compared with clinical observations. The time-resolved thrombus formation taking place in a fraction of the field of view was video recorded using a Peltier-cooled CCD camera. This vessel occlusion in the CAM model was reproducible and, in many ways, similar to that observed in the clinical use of verteporfin. The real-time video recording permitted the monitoring of platelet aggregation and revealed size-selective vascular closure as well as some degree of vasoconstriction. Platelets accumulated at intravascular junctions within seconds after verteporfin light activation, and capillaries were found to be closed 15 min later at the applied conditions. Larger-diameter vessels remained patent. Repetition of these data with a much more sensitive camera revealed occlusion of the treated area after 5 min with doses of verteporfin and light similar to those used clinically. Consequently, newly developed light-activated drugs can now be studied under clinically relevant conditions
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