Simultaneous deployment and tracking multi-robot strategies with connectivity maintenance

Multi-robot teams composed of ground and aerial vehicles have gained attention during the last few years. We present a scenario where both types of robots must monitor the same area from different view points. In this paper, we propose two Lloyd-based tracking strategies to allow the ground robots (agents) to follow the aerial ones (targets), keeping the connectivity between the agents. The first strategy establishes density functions on the environment so that the targets acquire more importance than other zones, while the second one iteratively modifies the virtual limits of the working area depending on the positions of the targets. We consider the connectivity maintenance due to the fact that coverage tasks tend to spread the agents as much as possible, which is addressed by restricting their motions so that they keep the links of a minimum spanning tree of the communication graph. We provide a thorough parametric study of the performance of the proposed strategies under several simulated scenarios. In addition, the methods are implemented and tested using realistic robotic simulation environments and real experiments

The blockchain: a new framework for robotic swarm systems

Swarms of robots will revolutionize many industrial applications, from targeted material delivery to precision farming. However, several of the heterogeneous characteristics that make them ideal for certain future applications --- robot autonomy, decentralized control, collective emergent behavior, etc. --- hinder the evolution of the technology from academic institutions to real-world problems. Blockchain, an emerging technology originated in the Bitcoin field, demonstrates that by combining peer-to-peer networks with cryptographic algorithms a group of agents can reach an agreement on a particular state of affairs and record that agreement without the need for a controlling authority. The combination of blockchain with other distributed systems, such as robotic swarm systems, can provide the necessary capabilities to make robotic swarm operations more secure, autonomous, flexible and even profitable. This work explains how blockchain technology can provide innovative solutions to four emergent issues in the swarm robotics research field. New security, decision making, behavior differentiation and business models for swarm robotic systems are described by providing case scenarios and examples. Finally, limitations and possible future problems that arise from the combination of these two technologies are described

Predicting cancer involvement of genes from heterogeneous data

<p>Abstract</p> <p>Background</p> <p>Systematic approaches for identifying proteins involved in different types of cancer are needed. Experimental techniques such as microarrays are being used to characterize cancer, but validating their results can be a laborious task. Computational approaches are used to prioritize between genes putatively involved in cancer, usually based on further analyzing experimental data.</p> <p>Results</p> <p>We implemented a systematic method using the PIANA software that predicts cancer involvement of genes by integrating heterogeneous datasets. Specifically, we produced lists of genes likely to be involved in cancer by relying on: (i) protein-protein interactions; (ii) differential expression data; and (iii) structural and functional properties of cancer genes. The integrative approach that combines multiple sources of data obtained positive predictive values ranging from 23% (on a list of 811 genes) to 73% (on a list of 22 genes), outperforming the use of any of the data sources alone. We analyze a list of 20 cancer gene predictions, finding that most of them have been recently linked to cancer in literature.</p> <p>Conclusion</p> <p>Our approach to identifying and prioritizing candidate cancer genes can be used to produce lists of genes likely to be involved in cancer. Our results suggest that differential expression studies yielding high numbers of candidate cancer genes can be filtered using protein interaction networks. </p

Human Cancer Protein-Protein Interaction Network: A Structural Perspective

Protein-protein interaction networks provide a global picture of cellular function and biological processes. Some proteins act as hub proteins, highly connected to others, whereas some others have few interactions. The dysfunction of some interactions causes many diseases, including cancer. Proteins interact through their interfaces. Therefore, studying the interface properties of cancer-related proteins will help explain their role in the interaction networks. Similar or overlapping binding sites should be used repeatedly in single interface hub proteins, making them promiscuous. Alternatively, multi-interface hub proteins make use of several distinct binding sites to bind to different partners. We propose a methodology to integrate protein interfaces into cancer interaction networks (ciSPIN, cancer structural protein interface network). The interactions in the human protein interaction network are replaced by interfaces, coming from either known or predicted complexes. We provide a detailed analysis of cancer related human protein-protein interfaces and the topological properties of the cancer network. The results reveal that cancer-related proteins have smaller, more planar, more charged and less hydrophobic binding sites than non-cancer proteins, which may indicate low affinity and high specificity of the cancer-related interactions. We also classified the genes in ciSPIN according to phenotypes. Within phenotypes, for breast cancer, colorectal cancer and leukemia, interface properties were found to be discriminating from non-cancer interfaces with an accuracy of 71%, 67%, 61%, respectively. In addition, cancer-related proteins tend to interact with their partners through distinct interfaces, corresponding mostly to multi-interface hubs, which comprise 56% of cancer-related proteins, and constituting the nodes with higher essentiality in the network (76%). We illustrate the interface related affinity properties of two cancer-related hub proteins: Erbb3, a multi interface, and Raf1, a single interface hub. The results reveal that affinity of interactions of the multi-interface hub tends to be higher than that of the single-interface hub. These findings might be important in obtaining new targets in cancer as well as finding the details of specific binding regions of putative cancer drug candidates

Identifying Hubs in Protein Interaction Networks

In spite of the scale-free degree distribution that characterizes most protein interaction networks (PINs), it is common to define an ad hoc degree scale that defines "hub" proteins having special topological and functional significance. This raises the concern that some conclusions on the functional significance of proteins based on network properties may not be robust.In this paper we present three objective methods to define hub proteins in PINs: one is a purely topological method and two others are based on gene expression and function. By applying these methods to four distinct PINs, we examine the extent of agreement among these methods and implications of these results on network construction.We find that the methods agree well for networks that contain a balance between error-free and unbiased interactions, indicating that the hub concept is meaningful for such networks

Spectators’ Negotiations of Risk, Masculinity and Performative Mobilities at the TT Races

This paper explores the particular assemblage of place, event and individual identity performances that occur each year in the Isle of Man in and through the TT (Tourist Trophy) motorcycle races. These road races are associated with a high degree of risk for the racers and the confluence of over 30,000 visitors and 10,000 motorcycles also presents potential risks for spectators and residents alike. Both motorcycling and risk-taking have been associated with particular forms of masculinity, notably hegemonic, working class and youthful masculinities. Using detailed surveys of spectators we argue that the TT races, while undoubtedly dominated by men and predicated on a cultural privileging of speed and skill, are grounded in varying combinations of determinate and reflexive attitudes to risk, reflecting the performance of a variety of gendered, ‘biker’ and wider identity-based positionalities. Findings also highlight a particular inter-relation of mobilities and place identities at the TT races and bring to light the highly significant and under-researched embodied, performative and emotional mobilities of spectators. The conceptual and methodological importance of (a) situated research of both mobilities and gender in specific place-temporalities and (b) wider surveys of motorcyclists to complement ethnographic studies of small cohorts are also stressed

Structure Collisions between Interacting Proteins

Protein-protein interactions take place at defined binding interfaces. One protein may bind two or more proteins at different interfaces at the same time. So far it has been commonly accepted that non-overlapping interfaces allow a given protein to bind other proteins simultaneously while no collisions occur between the binding protein structures. To test this assumption, we performed a comprehensive analysis of structural protein interactions to detect potential collisions. Our results did not indicate cases of biologically relevant collisions in the Protein Data Bank of protein structures. However, we discovered a number of collisions that originate from alternative protein conformations or quaternary structures due to different experimental conditions

cPath: open source software for collecting, storing, and querying biological pathways

BACKGROUND: Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. RESULTS: We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. CONCLUSION: cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling

Triangle network motifs predict complexes by complementing high-error interactomes with structural information

BackgroundA lot of high-throughput studies produce protein-protein interaction networks (PPINs) with many errors and missing information. Even for genome-wide approaches, there is often a low overlap between PPINs produced by different studies. Second-level neighbors separated by two protein-protein interactions (PPIs) were previously used for predicting protein function and finding complexes in high-error PPINs. We retrieve second level neighbors in PPINs, and complement these with structural domain-domain interactions (SDDIs) representing binding evidence on proteins, forming PPI-SDDI-PPI triangles.ResultsWe find low overlap between PPINs, SDDIs and known complexes, all well below 10%. We evaluate the overlap of PPI-SDDI-PPI triangles with known complexes from Munich Information center for Protein Sequences (MIPS). PPI-SDDI-PPI triangles have ~20 times higher overlap with MIPS complexes than using second-level neighbors in PPINs without SDDIs. The biological interpretation for triangles is that a SDDI causes two proteins to be observed with common interaction partners in high-throughput experiments. The relatively few SDDIs overlapping with PPINs are part of highly connected SDDI components, and are more likely to be detected in experimental studies. We demonstrate the utility of PPI-SDDI-PPI triangles by reconstructing myosin-actin processes in the nucleus, cytoplasm, and cytoskeleton, which were not obvious in the original PPIN. Using other complementary datatypes in place of SDDIs to form triangles, such as PubMed co-occurrences or threading information, results in a similar ability to find protein complexes.ConclusionGiven high-error PPINs with missing information, triangles of mixed datatypes are a promising direction for finding protein complexes. Integrating PPINs with SDDIs improves finding complexes. Structural SDDIs partially explain the high functional similarity of second-level neighbors in PPINs. We estimate that relatively little structural information would be sufficient for finding complexes involving most of the proteins and interactions in a typical PPIN