Search

Predicting the physical or functional associations through protein-protein interactions (PPIs) represents an integral approach for inferring novel protein functions and discovering new drug targets during repositioning analysis. Recent advances in high-throughput data generation and multi-omics techniques have enabled large-scale PPI predictions, thus promoting several computational methods based on different levels of biological evidence. However, integrating multiple results and strategies to optimize, extract interaction features automatically and scale up the entire PPI prediction process is still challenging. Most procedures do not offer an in-silico validation process to evaluate the predicted PPIs. In this context, this paper presents the PredPrIn scientific workflow that enables PPI prediction based on multiple lines of evidence, including the structure, sequence, and functional annotation categories, by combining boosting and stacking machine learning techniques. We also present a pipeline (PPIVPro) for the validation process based on cellular co-localization filtering and a focused search of PPI evidence on scientific publications. Thus, our combined approach provides means to extensive scale training or prediction of new PPIs and a strategy to evaluate the prediction quality. PredPrIn and PPIVPro are publicly available at https://github.com/YasCoMa/predprin and https://github.com/YasCoMa/ppi_validation_process.

In recent years, information-centric networks (ICNs) have gained attention from the research and industry communities as an efficient and reliable content distribution network paradigm, especially to address content-centric and bandwidth-needed applications together with the heterogeneous requirements of emergent networks, such as the Internet of Things (IoT), Vehicular Ad-hoc NETwork (VANET) and Mobile Edge Computing (MEC). In-network caching is an essential part of ICN architecture design, and the performance of the overall network relies on caching policy efficiency. Therefore, a large number of cache replacement strategies have been proposed to suit the needs of different networks. The literature extensively presents studies on the performance of the replacement schemes in different contexts. The evaluations may present different variations of context characteristics leading to different impacts on the performance of the policies or different results of most suitable policies. Conversely, there is a lack of research efforts to understand how the context characteristics influence policy performance. In this direction, we conducted an extensive study of the ICN literature through a Systematic Literature Review (SLR) process to map reported evidence of different aspects of context regarding the cache replacement schemes. Our main findings contribute to the understanding of what is a context from the perspective of cache replacement policies and the context characteristics that influence cache behavior. We also provide a helpful classification of policies based on context dimensions used to determine the relevance of contents. Further, we contribute with a set of cache-enabled networks and their respective context characteristics that enhance the cache eviction process.

In this article, we investigate limitations of importing methods based on algorithmic information theory from monoplex networks into multidimensional networks (such as multilayer networks) that have a large number of extra dimensions (i.e., aspects). In the worst-case scenario, it has been previously shown that node-aligned multidimensional networks with non-uniform multidimensional spaces can display exponentially larger algorithmic information (or lossless compressibility) distortions with respect to their isomorphic monoplex networks, so that these distortions grow at least linearly with the number of extra dimensions. In the present article, we demonstrate that node-unaligned multidimensional networks, either with uniform or non-uniform multidimensional spaces, can also display exponentially larger algorithmic information distortions with respect to their isomorphic monoplex networks. However, unlike the node-aligned non-uniform case studied in previous work, these distortions in the node-unaligned case grow at least exponentially with the number of extra dimensions. On the other hand, for node-aligned multidimensional networks with uniform multidimensional spaces, we demonstrate that any distortion can only grow up to a logarithmic order of the number of extra dimensions. Thus, these results establish that isomorphisms between finite multidimensional networks and finite monoplex networks do not preserve algorithmic information in general and highlight that the algorithmic information of the multidimensional space itself needs to be taken into account in multidimensional network complexity analysis.

We present the algebraic representation and basic algorithms for MultiAspect Graphs (MAGs). A MAG is a structure capable of representing multilayer and time-varying networks, as well as higher-order networks, while also having the property of being isomorphic to a directed graph. In particular, we show that, as a consequence of the properties associated with the MAG structure, a MAG can be represented in matrix form. Moreover, we also show that any possible MAG function (algorithm) can be obtained from this matrix-based representation. This is an important theoretical result since it paves the way for adapting well-known graph algorithms for application in MAGs. We present a set of basic MAG algorithms, constructed from well-known graph algorithms, such as degree computing, Breadth First Search (BFS), and Depth First Search (DFS). These algorithms adapted to the MAG context can be used as primitives for building other more sophisticated MAG algorithms. Therefore, such examples can be seen as guidelines on how to properly derive MAG algorithms from basic algorithms on directed graphs. We also make available Python implementations of all the algorithms presented in this paper.

The latest population-based studies in the medical literature worldwide indicate that acute myocardial infarction (AMI) patients still experience prolonged delay to be rescued, which often results in morbidity and mortality. This paper reports from a technological standpoint a teleconsultation and monitoring system named AToMS. This system addresses the problem of prehospital delivery of thrombolysis to AMI patients by enabling the remote interaction of the paramedics and a cardiologist available at a Coronary Care Unit (CCU). Such interaction allows the diagnosis of the patient eligibility to the immediate application of thrombolysis, which is meant to reduce the delay between the onset of symptoms and the eventual application of proper treatment. Such delay reduction is meant to increase the AMI patient's chances of survival and decrease the risks of postinfarction sequels. The teleconsultation is held with the support of wireless and mobile technologies, which also allows the cardiologist to monitor the patient while he/she is being taken to the nearest CCU. All exchanged messages among paramedics and cardiologists are recorded to render an auditable system. AToMS has been deployed in a first stage in the city of Rio de Janeiro, where the medical team involved in the project has conducted commissioned tests.