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

Critical Cooperation Range to Improve Spatial Network Robustness

A robust worldwide air-transportation network (WAN) is one that minimizes the number of stranded passengers under a sequence of airport closures. Building on top of this realistic example, here we address how spatial network robustness can profit from cooperation between local actors. We swap a series of links within a certain distance, a cooperation range, while following typical constraints of spatially embedded networks. We find that the network robustness is only improved above a critical cooperation range. Such improvement can be described in the framework of a continuum transition, where the critical exponents depend on the spatial correlation of connected nodes. For the WAN we show that, except for Australia, all continental networks fall into the same universality class. Practical implications of this result are also discussed

Breathing synchronization in interconnected networks

Global synchronization in a complex network of oscillators emerges from the interplay between its topology and the dynamics of the pairwise interactions among its numerous components. When oscillators are spatially separated, however, a time delay appears in the interaction which might obstruct synchronization. Here we study the synchronization properties of interconnected networks of oscillators with a time delay between networks and analyze the dynamics as a function of the couplings and communication lag. We discover a new breathing synchronization regime, where two groups appear in each network synchronized at different frequencies. Each group has a counterpart in the opposite network, one group is in phase and the other in anti-phase with their counterpart. For strong couplings, instead, networks are internally synchronized but a phase shift between them might occur. The implications of our findings on several socio-technical and biological systems are discussed.Comment: 7 pages, 3 figures + 3 pages of Supplemental Materia

Directed Random Markets: Connectivity determines Money

Boltzmann-Gibbs distribution arises as the statistical equilibrium probability distribution of money among the agents of a closed economic system where random and undirected exchanges are allowed. When considering a model with uniform savings in the exchanges, the final distribution is close to the gamma family. In this work, we implement these exchange rules on networks and we find that these stationary probability distributions are robust and they are not affected by the topology of the underlying network. We introduce a new family of interactions: random but directed ones. In this case, it is found the topology to be determinant and the mean money per economic agent is related to the degree of the node representing the agent in the network. The relation between the mean money per economic agent and its degree is shown to be linear.Comment: 14 pages, 6 figure

Quantifying responses of dung beetles to fire disturbance in tropical forests:the importance of trapping method and seasonality

Understanding how biodiversity responds to environmental changes is essential to provide the evidence-base that underpins conservation initiatives. The present study provides a standardized comparison between unbaited flight intercept traps (FIT) and baited pitfall traps (BPT) for sampling dung beetles. We examine the effectiveness of the two to assess fire disturbance effects and how trap performance is affected by seasonality. The study was carried out in a transitional forest between Cerrado (Brazilian Savanna) and Amazon Forest. Dung beetles were collected during one wet and one dry sampling season. The two methods sampled different portions of the local beetle assemblage. Both FIT and BPT were sensitive to fire disturbance during the wet season, but only BPT detected community differences during the dry season. Both traps showed similar correlation with environmental factors. Our results indicate that seasonality had a stronger effect than trap type, with BPT more effective and robust under low population numbers, and FIT more sensitive to fine scale heterogeneity patterns. This study shows the strengths and weaknesses of two commonly used methodologies for sampling dung beetles in tropical forests, as well as highlighting the importance of seasonality in shaping the results obtained by both sampling strategies

The zero-inflated promotion cure rate model applied to financial data on time-to-default

In this paper, we extend the promotion cure rate model studied in Yakovlev and Tsodikov (1996) and Chen et al. (1999) by incorporating an excess of zeros in the modeling. Despite relating covariates to the cure fraction, the current approach does not enable us to relate covariates to the fraction of zeros. The presence of excess of zeros in credit risk survival data stems from a group of loans that became defaulted shortly after the granting process. Through our proposal, all survival data available of customers is modeled with a multinomial logistic link for the three classes of banking customers: (i) individual with an event at the starting time (zero time), (ii) non-susceptible for the event, or (iii) susceptible for the event. The model parameter estimation is reached by the maximum likelihood estimation procedure and Monte Carlo simulations are carried out to assess its finite sample performance

Do space-for-time assessments underestimate the impacts of logging on tropical biodiversity? An Amazonian case study using dung beetles

Summary Human alteration of the global environment is leading to a pervasive loss of biodiversity. Most studies evaluating human impacts on biodiversity occur after the disturbance has taken place using spatially distinct sites to determine the undisturbed reference condition. This approach is known as a space‐for‐time (SFT) substitution. However, SFT substitution could be underestimating biodiversity loss if spatial controls fail to provide adequate inferences about pre‐disturbance conditions. We compare the SFT substitution with a before–after control–impact (BACI) approach by assessing dung beetles before and after a logging exploration in the Brazilian Amazon. We sampled 34 logging management units, of which 29 were selectively logged with different intensities after our first collection. We used dung beetle species richness, species composition and biomass as our biodiversity response metrics and the gradient of selective logging intensity as our explanatory metric. Only the BACI approach consistently demonstrated the negative impacts of logging intensification on all dung beetle community metrics. Moreover, the BACI approach explained significantly more of the variance in all the relationships and it doubled the estimates of species loss along the gradient of logging intensity when compared to SFT. Synthesis and applications. Our results suggest that space‐for‐time (SFT) substitution may greatly underestimate the consequences on local species diversity and community turnover. These results have important implications for researchers investigating human impacts on biodiversity. Incentivizing before–after control–impact (BACI) approaches will require longer‐term funding to gather the data and stronger links between researchers and landowners. However, BACI approaches are accompanied by many logistical constraints, making the continued use of SFT studies inevitable in many cases. We highlight that non‐significant results and weak effects should be viewed with caution. </jats:p

Efeito da densidade do solo na incidência de Fusarium spp.

O objetivo deste trabalho foi avaliar o efeito da densidade do solo resultante de dois sistemas de manejo e seis rotações de culturas na população de Fusarium spp