Silvana Rossetto

Intrusion Detection System for Wireless Sensor Networks Using Danger Theory Immune-Inspired Techniques

An IDS framework inspired in the Human Immune System to be applied in the wireless sensor network context is proposed. It uses an improved decentralized and customized version of the Dendritic Cell Algorithm, which allows nodes to monitor their neighborhood and collaborate to identify an intruder. The work was implemented and tested both in simulation and in real sensor platform scenarios, comparing them to each other and was also compared to a Negative Selection Theory implementation in order to demonstrate its efficiency in detecting a denial-of-sleep attack and in energy consumption. Results demonstrated the success of the proposal.

Increased ribosome density associated to positively charged residues is evident in ribosome profiling experiments performed in the absence of translation inhibitors.

ABSTRACT It has been proposed that polybasic peptides cause slower movement of ribosomes through an electrostatic interaction with the highly negative ribosome exit tunnel. Ribosome profiling data—the sequencing of short ribosome-bound fragments of mRNA—is a powerful tool for the analysis of mRNA translation. Using the yeast Saccharomyces cerevisiae as a model, we showed that reduced translation efficiency associated with polybasic protein sequences could be inferred from ribosome profiling. However, an increase in ribosome density at polybasic sequences was evident only when the commonly used translational inhibitors cycloheximide and anisomycin were omitted during mRNA isolation. Since ribosome profiling performed without inhibitors agrees with experimental evidence obtained by other methods, we conclude that cycloheximide and anisomycin must be avoided in ribosome profiling experiments.

Protein charge distribution in proteomes and its impact on translation

As proteins are synthesized, the nascent polypeptide must pass through a negatively charged exit tunnel. During this stage, positively charged stretches can interact with the ribosome walls and slow the translation. Therefore, charged polypeptides may be important factors that affect protein expression. To determine the frequency and distribution of positively and negatively charged stretches in different proteomes, the net charge was calculated for every 30 consecutive amino acid residues, which corresponds to the length of the ribosome exit tunnel. The following annotated and reviewed proteins in the UniProt database (Swiss-Prot) were analyzed: 551,705 proteins from different organisms and a total of 180 million protein segments. We observed that there were more negative than positive stretches and that super-charged positive sequences (i.e., net charges ≥ 14) were underrepresented in the proteomes. Overall, the proteins were more positively charged at their N-termini and C-termini, and this feature was present in most organisms and subcellular localizations. To investigate whether the N-terminal charges affect the elongation rates, previously published ribosomal profiling data obtained from S. cerevisiae, without translation-interfering drugs, were analyzed. We observed a nonlinear effect of the charge on the ribosome occupancy in which values ≥ +5 and ≤ -6 showed increased and reduced ribosome densities, respectively. These groups also showed different distributions across 80S monosomes and polysomes. Basic polypeptides are more common within short proteins that are translated by monosomes, whereas negative stretches are more abundant in polysome-translated proteins. These findings suggest that the nascent peptide charge impacts translation and can be one of the factors that regulate translation efficiency and protein expression.

The Design and Implementation of the Synchronous Language CÉU

CéU is a synchronous language targeting soft real-time systems. It is inspired by Esterel and has a simple semantics with fine-grain control over program execution. CéU uses an event-triggered notion of time that enables compile-time checks to detect conflicting concurrent statements, resulting in deterministic and concurrency-safe programs. We present the particularities of our design in comparison to Esterel, such as stack-based internal events, concurrency checks, safe integration with C, and first-class timers. We also present two implementation back ends: one aiming for resource efficiency and interoperability with C, and another as a virtual machine that allows remote reprogramming.

Terra: Flexibility and Safety in Wireless Sensor Networks

Terra is a system for programming wireless sensor network (WSN) applications. It combines the use of configurable virtual machines with a reactive scripting language that can be statically analyzed to avoid unbounded execution and memory conflicts. This approach allows the flexibility of remotely uploading code on motes to be combined with a set of guarantees for the programmer. The choice of the specific set of components in a virtual machine configuration defines the abstraction level seen by the application script. We describe a specific component library built for Terra, which we designed taking into account the functionality commonly needed in WSN applications—typically for sense and control. We also discuss the programming environment resulting from the combination of a statically analyzable scripting language with this library of components. Finally, we evaluate Terra by measuring its overhead in a basic application and discussing its use and cost in a typical monitoring WSN scenario.

Damage prediction for wind turbines using wireless sensor and actuator networks

The depletion of oil and gas reserves is bringing up economic, political and social issues which encourage the adoption of renewable, green energy sources. Wind energy is a major source of renewable energy because of the maturity and competitive costs of technological solutions to exploit this type of green energy. This kind of power generation is achieved through the use of wind turbines, which convert translational kinetic energy into rotational kinetic energy. The benefits already proven of this type of renewable energy source have motivated nations worldwide to adopt policies to improve the use of wind energy in order to minimize their dependence on oil and natural gas. However, the adoption of wind turbines poses several challenges. A key challenge is properly and timely identifying structural damages which affect the structural health of the wind turbine. In this context, we propose a damage prediction system for wind turbines based on wireless sensor and actuator network. The proposed system, called Delphos, is a decentralized system where all decision-making process is performed within the network, in a collaborative way by the nodes. The purpose of Delphos is to accurately predict when the turbine will reach a damage state, thus allowing timely actions on the turbine operation to prevent accidents, reducing maintenance costs and delays in the power generation. Delphos relies on a time series forecasting model, called ARIMA, and a fuzzy system to eliminate the influence of temperature in the process of damage prediction.

Distributed Systems with Wireless Sensor Networks

Conventional distributed system courses follow a syllabus in which a list of topics is discussed independently and at different levels of abstractions. We propose to use a wireless sensor network environment to pin all topics down to concrete applications and to maintain issues such as fault tolerance and coordination continuously present. We describe a syllabus with eight conceptual modules, each of them associated to a hands-on experience with wireless sensor networks, which may be assigned either as homework or as a hands-on class, depending on the number of classroom hours that are available.

Codon stabilization coefficient as an index for prediction of codon bias and its potential applications.

Different methods of mRNA half-life measurements are available, but genome-wide measurements of mRNA half-life in yeast showed a weak correlation between the methods. Moreover, when we compared mRNA half-life determined by these methods with other cellular measurements such as mRNA and protein abundance low correlation was found. To clarify this matter, we analyzed mRNA half-life datasets from nine different groups to determine the most accurate method of measurement. Since codon optimality is one of the significant determinants of mRNA stability, we used the codon stabilization coefficient (CSC) as a reference for mRNA half-life measurement accuracy. After CSC calculation for each dataset, we find strong positive correlations between the CSC from some datasets with other parameters that reflect codon optimality such as tRNA abundance and ribosome residence time. By the use of CSC parameter, we observed that most genes contain non-optimal codons and that codon bias exists toward optimized and non-optimized genes. We also observed that stretches of non-optimal are not randomly distributed since it causes impacts on translation.

Modeling and automatic code generation for wireless sensor network applications using model-driven or business process approaches: A systematic mapping study

Abstract This systematic mapping study investigates the modeling and automatic code generation initiatives for wireless sensor network applications based on the IEEE 802.15.4 standard, trying to understand the reasons, characteristics and methods used in the approaches available in the scientific literature, identifying research gaps and potential approaches that can be better exploited, indicating new possibilities of research. The focus is on studies that follow the Model-Driven or Business Process approaches.