A Monte Carlo Approach to Measure the Robustness of Boolean Networks

Emergence of robustness in biological networks is a paramount feature of evolving organisms, but a study of this property in vivo, for any level of representation such as Genetic, Metabolic, or Neuronal Networks, is a very hard challenge. In the case of Genetic Networks, mathematical models have been used in this context to provide insights on their robustness, but even in relatively simple formulations, such as Boolean Networks (BN), it might not be feasible to compute some measures for large system sizes. We describe in this work a Monte Carlo approach to calculate the size of the largest basin of attraction of a BN, which is intrinsically associated with its robustness, that can be used regardless the network size. We show the stability of our method through finite-size analysis and validate it with a full search on small networks.Comment: on 1st International Workshop on Robustness and Stability of Biological Systems and Computational Solutions (WRSBS

Sanitizing the fortress: protection of ant brood and nest material by worker antibiotics

Social groups are at particular risk for parasite infection, which is heightened in eusocial insects by the low genetic diversity of individuals within a colony. To combat this, adult ants have evolved a suite of defenses to protect each other, including the production of antimicrobial secretions. However, it is the brood in a colony that are most vulnerable to parasites because their individual defenses are limited, and the nest material in which ants live is also likely to be prone to colonization by potential parasites. Here, we investigate in two ant species whether adult workers use their antimicrobial secretions not only to protect each other but also to sanitize the vulnerable brood and nest material. We find that, in both leaf-cutting ants and weaver ants, the survival of the brood was reduced and the sporulation of parasitic fungi from them increased, when the workers nursing them lacked functional antimicrobial-producing glands. This was the case for both larvae that were experimentally treated with a fungal parasite (Metarhizium) and control larvae which developed infections of an opportunistic fungal parasite (Aspergillus). Similarly, fungi were more likely to grow on the nest material of both ant species if the glands of attending workers were blocked. The results show that the defense of brood and sanitization of nest material are important functions of the antimicrobial secretions of adult ants and that ubiquitous, opportunistic fungi may be a more important driver of the evolution of these defenses than rarer, specialist parasites

Event-Driven Network Programming

Software-defined networking (SDN) programs must simultaneously describe static forwarding behavior and dynamic updates in response to events. Event-driven updates are critical to get right, but difficult to implement correctly due to the high degree of concurrency in networks. Existing SDN platforms offer weak guarantees that can break application invariants, leading to problems such as dropped packets, degraded performance, security violations, etc. This paper introduces EVENT-DRIVEN CONSISTENT UPDATES that are guaranteed to preserve well-defined behaviors when transitioning between configurations in response to events. We propose NETWORK EVENT STRUCTURES (NESs) to model constraints on updates, such as which events can be enabled simultaneously and causal dependencies between events. We define an extension of the NetKAT language with mutable state, give semantics to stateful programs using NESs, and discuss provably-correct strategies for implementing NESs in SDNs. Finally, we evaluate our approach empirically, demonstrating that it gives well-defined consistency guarantees while avoiding expensive synchronization and packet buffering

Walk on the wild side: Temporarily unstable paths and multiplicative sunspots

We propose a generalization of the rational expectations framework to allow for temporarily unstable paths. Our approach introduces multiplicative sunspot shocks and it yields drifting parameters and stochastic volatility. Then, we provide an econometric strategy to estimate this generalized model on the data. The methodology allows the data to choose between different possible alternatives: determinacy, indeterminacy, and temporary instability. We apply our methodology to US in?ation dynamics in the 1970s through the lens of a simple New Keynesian model. When temporarily unstable paths are allowed, the data unambiguously select them to explain the stag?ation period in the 1970s

Vanishing Viscosity Limits and Boundary Layers for Circularly Symmetric 2D Flows

We continue the work of Lopes Filho, Mazzucato and Nussenzveig Lopes [LMN], on the vanishing viscosity limit of circularly symmetric viscous flow in a disk with rotating boundary, shown there to converge to the inviscid limit in $L^2$-norm as long as the prescribed angular velocity $\alpha(t)$ of the boundary has bounded total variation. Here we establish convergence in stronger $L^2$ and $L^p$-Sobolev spaces, allow for more singular angular velocities $\alpha$, and address the issue of analyzing the behavior of the boundary layer. This includes an analysis of concentration of vorticity in the vanishing viscosity limit. We also consider such flows on an annulus, whose two boundary components rotate independently. [LMN] Lopes Filho, M. C., Mazzucato, A. L. and Nussenzveig Lopes, H. J., Vanishing viscosity limit for incompressible flow inside a rotating circle, preprint 2006

Costs and externalities of road transport in Portugal

Urban dispersion (sprawl) is a reality, however unplanned it may be. Its supporters advocate contact with nature, space and intimacy, however disadvantages include land consumption, public infrastructure and mobility costs and housing prices. The Research Project “Costs and Benefits of Urban Dispersion on a local scale” seeks to contribute to the debate with an objective approach based on the quantification of costs, externalities and benefits of different urban settlement patterns. This paper presents one of the Project’s tasks, the one concerning mobility costs, including externalities. Quantified costs include investment, inspection, insurance, energy and maintenance, as well as external social and environmental costs for road transport, the most significant transport mode operating on a local scale. Different methods are combined depending on available data sources in order to achieve figures for each of the cost components per vehicle-km, ton-km and passenger-km at prices of 2005. Preliminary results for direct costs suggest that in light vehicles investment costs are responsible for the largest share of the totals, while energy costs are the most relevant cost component in heavy vehicles. Heavy duty passenger transport is significantly more expensive than their counterparts. Externalities may mount up to around half of the total costs for some road vehicles.publishe

The role of bacteria in pine wilt disease: insights from microbiome analysis.

Pine Wilt Disease (PWD) has a significant impact on Eurasia pine forests. The microbiome of the nematode (the primary cause of the disease), its insect vector, and the host tree may be relevant for the disease mechanism. The aim of this study was to characterize these microbiomes, from three PWD-affected areas in Portugal, using Denaturing Gradient Gel Electrophoresis, 16S rRNA gene pyrosequencing, and a functional inference-based approach (PICRUSt). The bacterial community structure of the nematode was significantly different from the infected trees but closely related to the insect vector, supporting the hypothesis that the nematode microbiome might be in part inherited from the insect. Sampling location influenced mostly the tree microbiome (P < 0.05). Genes related both with plant growth promotion and phytopathogenicity were predicted for the tree microbiome. Xenobiotic degradation functions were predicted in the nematode and insect microbiomes. Phytotoxin biosynthesis was also predicted for the nematode microbiome, supporting the theory of a direct contribution of the microbiome to tree-wilting. This is the first study that simultaneously characterized the nematode, tree and insect-vector microbiomes from the same affected areas, and overall the results support the hypothesis that the PWD microbiome plays an important role in the disease's development

Instanton Corrected Non-Supersymmetric Attractors

We discuss non-supersymmetric attractors with an instanton correction in Type IIA string theory compactified on a Calabi-Yau three-fold at large volume. For a stable non-supersymmetric black hole, the attractor point must minimize the effective black hole potential. We study the supersymmetric as well as non-supersymmetric attractors for the D0-D4 system with instanton corrections. We show that in simple models, like the STU model, the flat directions of the mass matrix can be lifted by a suitable choice of the instanton parameters.Comment: Minor modifications, Corrected typos, 38 pages, 1 figur