5,388 research outputs found
A polynomial eigenvalue approach for multiplex networks
We explore the block nature of the matrix representation of multiplex
networks, introducing a new formalism to deal with its spectral properties as a
function of the inter-layer coupling parameter. This approach allows us to
derive interesting results based on an interpretation of the traditional
eigenvalue problem. More specifically, we reduce the dimensionality of our
matrices but increase the power of the characteristic polynomial, i.e, a
polynomial eigenvalue problem. Such an approach may sound counterintuitive at
first glance, but it allows us to relate the quadratic problem for a 2-Layer
multiplex system with the spectra of the aggregated network and to derive
bounds for the spectra, among many other interesting analytical insights.
Furthermore, it also permits to directly obtain analytical and numerical
insights on the eigenvalue behavior as a function of the coupling between
layers. Our study includes the supra-adjacency, supra-Laplacian, and the
probability transition matrices, which enable us to put our results under the
perspective of structural phases in multiplex networks. We believe that this
formalism and the results reported will make it possible to derive new results
for multiplex networks in the future.Comment: 15 pages including figures. Submitted for publicatio
On degree-degree correlations in multilayer networks
We propose a generalization of the concept of assortativity based on the
tensorial representation of multilayer networks, covering the definitions given
in terms of Pearson and Spearman coefficients. Our approach can also be applied
to weighted networks and provides information about correlations considering
pairs of layers. By analyzing the multilayer representation of the airport
transportation network, we show that contrasting results are obtained when the
layers are analyzed independently or as an interconnected system. Finally, we
study the impact of the level of assortativity and heterogeneity between layers
on the spreading of diseases. Our results highlight the need of studying
degree-degree correlations on multilayer systems, instead of on aggregated
networks.Comment: 8 pages, 3 figure
Layer degradation triggers an abrupt structural transition in multiplex networks
Network robustness is a central point in network science, both from a
theoretical and a practical point of view. In this paper, we show that layer
degradation, understood as the continuous or discrete loss of links' weight,
triggers a structural transition revealed by an abrupt change in the algebraic
connectivity of the graph. Unlike traditional single layer networks, multiplex
networks exist in two phases, one in which the system is protected from link
failures in some of its layers and one in which all the system senses the
failure happening in one single layer. We also give the exact critical value of
the weight of the intra-layer links at which the transition occurs for
continuous layer degradation and its relation to the value of the coupling
between layers. This relation allows us to reveal the connection between the
transition observed under layer degradation and the one observed under the
variation of the coupling between layers.Comment: 8 pages, and 8 figures in Revtex style. Submitted for publicatio
On the onset of synchronization of Kuramoto oscillators in scale-free networks
Despite the great attention devoted to the study of phase oscillators on
complex networks in the last two decades, it remains unclear whether scale-free
networks exhibit a nonzero critical coupling strength for the onset of
synchronization in the thermodynamic limit. Here, we systematically compare
predictions from the heterogeneous degree mean-field (HMF) and the quenched
mean-field (QMF) approaches to extensive numerical simulations on large
networks. We provide compelling evidence that the critical coupling vanishes as
the number of oscillators increases for scale-free networks characterized by a
power-law degree distribution with an exponent , in line
with what has been observed for other dynamical processes in such networks. For
, we show that the critical coupling remains finite, in agreement
with HMF calculations and highlight phenomenological differences between
critical properties of phase oscillators and epidemic models on scale-free
networks. Finally, we also discuss at length a key choice when studying
synchronization phenomena in complex networks, namely, how to normalize the
coupling between oscillators
Centrality anomalies in complex networks as a result of model over-simplification
Tremendous advances have been made in our understanding of the properties and
evolution of complex networks. These advances were initially driven by
information-poor empirical networks and theoretical analysis of unweighted and
undirected graphs. Recently, information-rich empirical data complex networks
supported the development of more sophisticated models that include edge
directionality and weight properties, and multiple layers. Many studies still
focus on unweighted undirected description of networks, prompting an essential
question: how to identify when a model is simpler than it must be? Here, we
argue that the presence of centrality anomalies in complex networks is a result
of model over-simplification. Specifically, we investigate the well-known
anomaly in betweenness centrality for transportation networks, according to
which highly connected nodes are not necessarily the most central. Using a
broad class of network models with weights and spatial constraints and four
large data sets of transportation networks, we show that the unweighted
projection of the structure of these networks can exhibit a significant
fraction of anomalous nodes compared to a random null model. However, the
weighted projection of these networks, compared with an appropriated null
model, significantly reduces the fraction of anomalies observed, suggesting
that centrality anomalies are a symptom of model over-simplification. Because
lack of information-rich data is a common challenge when dealing with complex
networks and can cause anomalies that misestimate the role of nodes in the
system, we argue that sufficiently sophisticated models be used when anomalies
are detected.Comment: 14 pages, including 9 figures. APS style. Accepted for publication in
New Journal of Physic
Disease Localization in Multilayer Networks
We present a continuous formulation of epidemic spreading on multilayer
networks using a tensorial representation, extending the models of monoplex
networks to this context. We derive analytical expressions for the epidemic
threshold of the SIS and SIR dynamics, as well as upper and lower bounds for
the disease prevalence in the steady state for the SIS scenario. Using the
quasi-stationary state method we numerically show the existence of disease
localization and the emergence of two or more susceptibility peaks, which are
characterized analytically and numerically through the inverse participation
ratio. Furthermore, when mapping the critical dynamics to an eigenvalue
problem, we observe a characteristic transition in the eigenvalue spectra of
the supra-contact tensor as a function of the ratio of two spreading rates: if
the rate at which the disease spreads within a layer is comparable to the
spreading rate across layers, the individual spectra of each layer merge with
the coupling between layers. Finally, we verified the barrier effect, i.e., for
three-layer configuration, when the layer with the largest eigenvalue is
located at the center of the line, it can effectively act as a barrier to the
disease. The formalism introduced here provides a unifying mathematical
approach to disease contagion in multiplex systems opening new possibilities
for the study of spreading processes.Comment: Revised version. 25 pages and 18 figure
Genomic analysis of eight native plasmids of the phytopathogen Pseudomonas syringae
Comunicación a conferenciaThe pPT23A family of plasmids (PFPs) appears to be indigenous to the plant pathogen Pseudomonas syringae and these plasmids are widely distributed and widely transferred among pathovars of P. syringae and related species. PFPs are sources of accessory genes for their hosts that can include genes important for virulence and epiphytic colonization of plant leaf surfaces. Further understanding of the evolution of the pPT23A plasmid family and the role of these plasmids in P. syringae biology and pathogenesis, requires the determination and analysis of additional complete, closed plasmid genome sequences. Therefore, our main objective was to obtain complete genome sequences from PFPs from three different P. syringae pathovars and perform a comparative genomic analysis. In this work plasmid DNA isolation, purification by CsCl-EtBr gradients, and sequencing using 454 platform, were used to obtain the complete sequence of P. syringae plasmids. Different bioinformatic tools were used to analyze the plasmid synteny, to identify virulence genes (i.e. type 3 effectors) and to unravel the evolutionary history of PFPs. Our sequence analysis revealed that PFPs from P. syringae encode suites of accessory genes that are selected at different levels (universal, interpathovar and intrapathovar). The conservation of type IVSS encoding conjugation functions also contributes to the distribution of these plasmids within P. syringae populations. Thus, this study contributes to unravel the genetic basis of the role of PFPs in different P. syringae lifestyles.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech
Isolation, characterization and selection of bacterial isolates from a suppressive soil with beneficial traits to plants
Backgrounds
This study focused on the characterization and selection of bacterial strains obtained from a suppressive soil displaying antifungal activity against the soilborne phytopathogenic fungi Rosellinia necatrix. Bacterial profile from this suppressive soil were first obtained by 16S rRNA gene sequencing, revealing a significant increase in the bacterial class Gammaproteobacteria, especially in some antagonistic representatives of Pseudomonas spp.
Objectives
To obtain and characterize a collection of 246 bacterial isolates obtained from this suppressive soil, in order to identify new strains with antifungal activity against fungal phytopathogens.
Methods
To obtain the bacterial collection, we performed an isolation on a selective medium for Pseudomonas-like microorganisms. Further characterization tests were used in order to analyse the bacterial collection, including identification of the general metabolic profile of glucose, the profiling of antifungals produced, including both the putative production of antifungal compounds and lytic exoenzymes, and the evaluation of traits related with beneficial effects on plants.
Conclusions
A final selection of representative strains resulted in antifungal isolates belonging to the genus Pseudomonas, but also some representatives of the genera Serratia and Stenotrophomonas. These selected strains were tested for plant protection by an in vivo experiment using avocado and wheat plants challenged by the pathogen R. necatrix, showing all of them an antifungal ability and plant disease protection.
Pseudomonas-like strains isolated from suppressive soils constitute an excellent source for novel microbial biocontrol agents against soilborne fungal pathogens.
This work was supported by grant AGL2014-52518-C2-1-R. Carmen Vida and Sandra Tienda are supported by a PhD fellowship from the FPI program of the Spanish Government.This work was supported by grant AGL2014-52518-C2-1-R. Carmen Vida and Sandra Tienda are supported by a PhD fellowship from the FPI program of the Spanish Government; Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech
Comparative genomic analysis of native pseudomonas syringae plasmids belonging to the ppt23 a family reveals their role in p. Syringae epiphytic and pathogenic lifestyles
Backgrounds
The pPT23A family of plasmids (PFPs) appears to be indigenous to the plant pathogen Pseudomonas syringae and these plasmids are widely distributed and widely transferred among pathovars of P. syringae and related species. PFPs are sources of accessory genes for their hosts that can include genes important for virulence and epiphytic colonization of plant leaf surfaces.
Objectives
Further understanding of the evolution of the pPT23A plasmid family and the role of these plasmids in P. syringae biology and pathogenesis, requires the determination and analysis of additional complete, closed plasmid genome sequences. Therefore, our main objective was to obtain complete genome sequences of PFPs from three different P. syringae pathovars and perform a comprehensive comparative genomic analysis.
Methods
In this work plasmid DNA isolation, purification by CsCl-EtBr gradients, and sequencing using 454 platform, were carried out to obtain the complete sequence of P. syringae plasmids. Different bioinformatic tools were used to analyze the plasmid synteny, to identify virulence genes (i.e. type 3 effectors) and to unravel the evolutionary history of PFPs.
Conclusions
Our sequence analysis revealed that PFPs from P. syringae encode suites of accessory genes that are selected at different levels (universal, interpathovar and intrapathovar). The conservation of type IVSS encoding conjugation functions also contributes to the distribution of these plasmids within P. syringae populations. Thus, this study contributes to unravel the genetic bases of the role of PFPs in different P. syringae lifestyles.
This work was supported by grants Proyecto de Excelencia, Junta de Andalucía (P07-AGR-02471; P12-AGR-1473) and by Michigan State University AgBioResearch.This work was supported by grants Proyecto de Excelencia, Junta de Andalucía (P07-AGR-02471; P12-AGR-1473) and by Michigan State University AgBioResearch; Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech
- …