Finding instabilities in the community structure of complex networks

The problem of finding clusters in complex networks has been extensively studied by mathematicians, computer scientists and, more recently, by physicists. Many of the existing algorithms partition a network into clear clusters, without overlap. We here introduce a method to identify the nodes lying ``between clusters'' and that allows for a general measure of the stability of the clusters. This is done by adding noise over the weights of the edges of the network. Our method can in principle be applied with any clustering algorithm, provided that it works on weighted networks. We present several applications on real-world networks using the Markov Clustering Algorithm (MCL).Comment: 4 pages, 5 figure

Suppression of the thermal hysteresis in magnetocaloric MnAs thin film by highly charged ion bombardment

We present the investigation on the modifications of structural and magnetic properties of MnAs thin film epitaxially grown on GaAs induced by slow highly charged ions bombardment under well-controlled conditions. The ion-induced defects facilitate the nucleation of one phase with respect to the other in the first-order magneto-structural MnAs transition with a consequent suppression of thermal hysteresis without any significant perturbation on the other structural and magnetic properties. In particular, the irradiated film keeps the giant magnetocaloric effect at room temperature opening new perspective on magnetic refrigeration technology for everyday use

Characterization and Modeling of DHBT in InP/GaAsSb Technology for the Design and Fabrication of a Ka Band MMIC Oscillator

This paper presents the design of an MMIC oscillator operating at a 38 GHz frequency. This circuit was fabricated by the III–V Lab with the new InP/GaAsSb Double Heterojunction Bipolar Transistor (DHBT) submicronic technology (We=700 nm). The transistor used in the circuit has a 15 μm long two-finger emitter. This paper describes the complete nonlinear modeling of this DHBT, including the cyclostationary modeling of its low frequency (LF) noise sources. The specific interest of the methodology used to design this oscillator resides in being able to choose a nonlinear operating condition of the transistor from an analysis in amplifier mode. The oscillator simulation and measurement results are compared. A 38 GHz oscillation frequency with 8.6 dBm output power and a phase noise of −80 dBc/Hz at 100 KHz offset from carrier have been measured

Modulating the phase transition temperature of giant magnetocaloric thin films by ion irradiation

Magnetic refrigeration based on the magnetocaloric effect at room temperature is one of the most attractive alternative to the current gas compression/expansion method routinely employed. Nevertheless, in giant magnetocaloric materials, optimal refrigeration is restricted to the narrow temperature window of the phase transition (Tc). In this work, we present the possibility of varying this transition temperature into a same giant magnetocaloric material by ion irradiation. We demonstrate that the transition temperature of iron rhodium thin films can be tuned by the bombardment of ions of Ne 5+ with varying fluences up to 10 14 ions cm --2 , leading to optimal refrigeration over a large 270--380 K temperature window. The Tc modification is found to be due to the ion-induced disorder and to the density of new point-like defects. The variation of the phase transition temperature with the number of incident ions opens new perspectives in the conception of devices using giant magnetocaloric materials

Magnetic properties changes of MnAs thin films irradiated with highly charged ions

We present the first investigation on the effect of highly charged ion bombardment on a manganese arsenide thin film. The MnAs films, 150 nm thick, are irradiated with 90 keV Ne$^{9+}$ ions with a dose varying from $1.6\times10^{12}$ to $1.6\times10^{15}$ ions/cm$^2$. The structural and magnetic properties of the film after irradiation are investigated using different techniques, namely, X-ray diffraction, magneto-optic Kerr effect and magnetic force microscope. Preliminary results are presented. From the study of the lattice spacing, we measure a change on the film structure that depends on the received dose, similarly to previous studies with other materials. Investigations on the surface show a strong modification of its magnetic properties

Comparative genomics study reveals Red Sea Bacillus with characteristics associated with potential microbial cell factories (MCFs)

© 2019, The Author(s). Recent advancements in the use of microbial cells for scalable production of industrial enzymes encourage exploring new environments for efficient microbial cell factories (MCFs). Here, through a comparison study, ten newly sequenced Bacillus species, isolated from the Rabigh Harbor Lagoon on the Red Sea shoreline, were evaluated for their potential use as MCFs. Phylogenetic analysis of 40 representative genomes with phylogenetic relevance, including the ten Red Sea species, showed that the Red Sea species come from several colonization events and are not the result of a single colonization followed by speciation. Moreover, clustering reactions in reconstruct metabolic networks of these Bacillus species revealed that three metabolic clades do not fit the phylogenetic tree, a sign of convergent evolution of the metabolism of these species in response to special environmental adaptation. We further showed Red Sea strains Bacillus paralicheniformis (Bac48) and B. halosaccharovorans (Bac94) had twice as much secreted proteins than the model strain B. subtilis 168. Also, Bac94 was enriched with genes associated with the Tat and Sec protein secretion system and Bac48 has a hybrid PKS/NRPS cluster that is part of a horizontally transferred genomic region. These properties collectively hint towards the potential use of Red Sea Bacillus as efficient protein secreting microbial hosts, and that this characteristic of these strains may be a consequence of the unique ecological features of the isolation environment

Atmospheric gas absorption knowledge in the submillimeter: Modeling, field measurements, and uncertainty quantification

Members of the atmospheric and astronomical science communities met to review the current state of the art of the submillimeter spectral region. Knowledge of gas spectroscopy is still questionable at these frequencies but is important to fully exploit upcoming meteorological satellite measurements

Present state of global wetland extent and wetland methane modelling: methodology of a model inter-comparison project (WETCHIMP)

The Wetland and Wetland CH4 Intercomparison of Models Project (WETCHIMP) was created to evaluate our present ability to simulate large-scale wetland characteristics and corresponding methane (CH4) emissions. A multi-model comparison is essential to evaluate the key uncertainties in the mechanisms and parameters leading to methane emissions. Ten modelling groups joined WETCHIMP to run eight global and two regional models with a common experimental protocol using the same climate and atmospheric carbon dioxide (CO2) forcing datasets. We reported the main conclusions from the intercomparison effort in a companion paper (Melton et al., 2013). Here we provide technical details for the six experiments, which included an equilibrium, a transient, and an optimized run plus three sensitivity experiments (temperature, precipitation, and atmospheric CO2 concentration). The diversity of approaches used by the models is summarized through a series of conceptual figures, and is used to evaluate the wide range of wetland extent and CH4 fluxes predicted by the models in the equilibrium run. We discuss relationships among the various approaches and patterns in consistencies of these model predictions. Within this group of models, there are three broad classes of methods used to estimate wetland extent: prescribed based on wetland distribution maps, prognostic relationships between hydrological states based on satellite observations, and explicit hydrological mass balances. A larger variety of approaches was used to estimate the net CH4 fluxes from wetland systems. Even though modelling of wetland extent and CH4 emissions has progressed significantly over recent decades, large uncertainties still exist when estimating CH4 emissions: there is little consensus on model structure or complexity due to knowledge gaps, different aims of the models, and the range of temporal and spatial resolutions of the models

Generation of recombinant single-chain antibodies neutralizing the cytolytic activity of vaginolysin, the main virulence factor of Gardnerella vaginalis

Generated scFvs is the first example of recombinant single-chain antibodies with VLY-neutralizing activity produced in prokaryote expression system. G. vaginalis caused infections continue to be a world-wide problem, therefore neutralizing recombinant antibodies may provide novel therapeutic agents useful in the treatment of bacterial vaginosis and other diseases caused by G. vaginalis

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks

International audienceIncreasing amounts of sequence data are becoming available for a wide range of non-model organisms. Investigating and modelling the metabolic behaviour of those organisms is highly relevant to understand their biology and ecology. As sequences are often incomplete and poorly annotated, draft networks of their metabolism largely suffer from incompleteness. Appropriate gap-filling methods to identify and add missing reactions are therefore required to address this issue. However, current tools rely on phenotypic or taxonomic information, or are very sensitive to the stoichiometric balance of metabolic reactions, especially concerning the co-factors. This type of information is often not available or at least prone to errors for newly-explored organisms. Here we introduce Meneco, a tool dedicated to the topological gap-filling of genome-scale draft metabolic networks. Meneco reformulates gap-filling as a qualitative combinatorial optimization problem, omitting constraints raised by the stoichiometry of a metabolic network considered in other methods, and solves this problem using Answer Set Programming. Run on several artificial test sets gathering 10,800 degraded Escherichia coli networks Meneco was able to efficiently identify essential reactions missing in networks at high degradation rates, outperforming the stoichiometry-based tools in scalability. To demonstrate the utility of Meneco we applied it to two case studies. Its application to recent metabolic networks reconstructed for the brown algal model Ectocarpus siliculosus and an associated bacterium Candidatus Phaeomarinobacter ectocarpi revealed several candidate metabolic pathways for algal-bacterial interactions. Then Meneco was used to reconstruct, from transcriptomic and metabolomic data, the first metabolic network for the microalga Euglena mutabilis. These two case studies show that Meneco is a versatile tool to complete draft genome-scale metabolic networks produced from heterogeneous data, and to suggest relevant reactions that explain the metabolic capacity of a biological system