The evolution of controlled multitasked gene networks: The role of introns and other noncoding RNAs in the development of complex organisms

Eukaryotic phenotypic diversity arises from multitasking of a core proteome of limited size. Multitasking is routine in computers, as well as in other sophisticated information systems, and requires multiple inputs and outputs to control and integrate network activity. Higher eukaryotes have a mosaic gene structure with a dual output, mRNA (protein-coding) sequences and introns, which are released from the pre-mRNA by posttranscriptional processing. Introns have been enormously successful as a class of sequences and comprise up to 95% of the primary transcripts of protein-coding genes in mammals. In addition, many other transcripts (perhaps more than half) do not encode proteins at all, but appear both to be developmentally regulated and to have genetic function. We suggest that these RNAs (eRNAs) have evolved to function as endogenous network control molecules which enable direct gene-gene communication and multitasking of eukaryotic genomes. Analysis of a range of complex genetic phenomena in which RNA is involved or implicated, including co-suppression, transgene silencing, RNA interference, imprinting, methylation, and transvection, suggests that a higher-order regulatory system based on RNA signals operates in the higher eukaryotes and involves chromatin remodeling as well as other RNA-DNA, RNA-RNA, and RNA-protein interactions. The evolution of densely connected gene networks would be expected to result in a relatively stable core proteome due to the multiple reuse of components, implying,that cellular differentiation and phenotypic variation in the higher eukaryotes results primarily from variation in the control architecture. Thus, network integration and multitasking using trans-acting RNA molecules produced in parallel with protein-coding sequences may underpin both the evolution of developmentally sophisticated multicellular organisms and the rapid expansion of phenotypic complexity into uncontested environments such as those initiated in the Cambrian radiation and those seen after major extinction events.

A model for heterogeneous networks management and Performance evaluation

In general, modern networks are analysed by taking several Key Performance Indicators (KPIs) into account, their proper balance being required in order to guarantee a desired Quality of Service (QoS), particularly, cellular wireless heterogeneous networks. A model to integrate a set of KPIs into a single one is presented, by using a Cost Function that includes these KPIs, providing for each network node a single evaluation parameter as output, and reflecting network conditions and common radio resource management strategies performance. The proposed model enables the implementation of different network management policies, by manipulating KPIs according to users' or operators' perspectives, allowing for a better QoS. Results show that different policies can in fact be established, with a different impact on the network, e.g., with median values ranging by a factor higher than two.

A Model to Evaluate Vertical Handovers on JRRM

In a heterogeneous cellular networks environment, users behaviour and network deployment configuration parameters have an impact on the overall Quality of Service. This paper proposes a new and simple model that, on the one hand, explores the users behaviour impact on the network by having mobility, multi-service usage and traffic generation profiles as inputs, and on the other, enables the network setup configuration evaluation impact on the Joint Radio Resource Management (JRRM), assessing some basic JRRM performance indicators, like Vertical Handover (VHO) probabilities, average bit rates, and number of active users, among others. VHO plays an important role in fulfilling seamless users sessions transfer when mobile terminals cross different Radio Access Technologies (RATs) boundaries. Results show that high bit rate RATs suffer and generate more influence from/on other RATs, by producing additional signalling traffic to a JRRM entity. Results also show that the VHOs probability can range from 5 up to 65%, depending on RATs cluster radius and users mobility profile.

A SON Enhanced Algorithm for Observed Time Differences Based Geolocation in Real 3G Networks

Conferência - 16th International Symposium on Wireless Personal Multimedia Communications (WPMC)- Jun 24-27, 2013

Engineering hybrid wired/wireless fieldbus networks - a case study

Advances in networking and information technologies are transforming factory-floor communication systems into a mainstream activity within industrial automation. It is now recognized that future industrial computer systems will be intimately tied to real-time computing and to communication technologies. For this vision to succeed, complex heterogeneous factory-floor communication networks (including mobile/wireless components) need to function in a predictable, flawless, efficient and interoperable way. In this paper we re-visit the issue of supporting real-time communications in hybrid wired/wireless fieldbus-based networks, bringing into it some experimental results obtained in the framework of the RFieldbus ISEP pilot.

Profibus protocol extensions for enabling inter-cell mobility in bridge-based hybrid wired/wireless networks

Future industrial control/multimedia applications will increasingly impose or benefit from wireless and mobile communications. Therefore, there is an enormous eagerness for extending currently available industrial communications networks with wireless and mobility capabilities. The RFieldbus European project is just one example, where a PROFIBUS-based hybrid (wired/wireless) architecture was specified and implemented. In the RFieldbus architecture, interoperability between wired and wireless components is achieved by the use specific intermediate networking systems operating at the physical layer level, i.e. operating as repeaters. Instead, in this paper we will focus on a bridge-based approach, which presents several advantages. This concept was introduced in (Ferreira, et al., 2002), where a bridge-based approach was briefly outlined. Then, a specific Inter-Domain Protocol (IDP) was proposed to handle the Inter-Domain transactions in such a bridge-based approach (Ferreira, et al., 2003a). The major contribution of this paper is in extending these previous works by describing the protocol extensions to support inter-cell mobility in such a bridge-based hybrid wired/wireless PROFIBUS networks.

Improving quality-of-service in wireless sensor networks by mitigating “Hidden-Node Collisions”

Wireless sensor networks (WSNs) emerge as underlying infrastructures for new classes of large-scale networked embedded systems. However, WSNs system designers must fulfill the quality-of-service (QoS) requirements imposed by the applications (and users). Very harsh and dynamic physical environments and extremely limited energy/computing/memory/communication node resources are major obstacles for satisfying QoS metrics such as reliability, timeliness, and system lifetime. The limited communication range of WSN nodes, link asymmetry, and the characteristics of the physical environment lead to a major source of QoS degradation in WSNs-the ldquohidden node problem.rdquo In wireless contention-based medium access control (MAC) protocols, when two nodes that are not visible to each other transmit to a third node that is visible to the former, there will be a collision-called hidden-node or blind collision. This problem greatly impacts network throughput, energy-efficiency and message transfer delays, and the problem dramatically increases with the number of nodes. This paper proposes H-NAMe, a very simple yet extremely efficient hidden-node avoidance mechanism for WSNs. H-NAMe relies on a grouping strategy that splits each cluster of a WSN into disjoint groups of non-hidden nodes that scales to multiple clusters via a cluster grouping strategy that guarantees no interference between overlapping clusters. Importantly, H-NAMe is instantiated in IEEE 802.15.4/ZigBee, which currently are the most widespread communication technologies for WSNs, with only minor add-ons and ensuring backward compatibility with their protocols standards. H-NAMe was implemented and exhaustively tested using an experimental test-bed based on ldquooff-the-shelfrdquo technology, showing that it increases network throughput and transmission success probability up to twice the values obtained without H-NAMe. H-NAMe effectiveness was also demonstrated in a target tracking application with mobile robots - over a WSN deployment.

Dimensioning and worst-case analysis of cluster-tree sensor networks

Modeling the fundamental performance limits of Wireless Sensor Networks (WSNs) is of paramount importance to understand their behavior under the worst-case conditions and to make the appropriate design choices. This is particular relevant for time-sensitive WSN applications, where the timing behavior of the network protocols (message transmission must respect deadlines) impacts on the correct operation of these applications. In that direction this paper contributes with a methodology based on Network Calculus, which enables quick and efficient worst-case dimensioning of static or even dynamically changing cluster-tree WSNs where the data sink can either be static or mobile. We propose closed-form recurrent expressions for computing the worst-case end-to-end delays, buffering and bandwidth requirements across any source-destination path in a cluster-tree WSN. We show how to apply our methodology to the case of IEEE 802.15.4/ZigBee cluster-tree WSNs. Finally, we demonstrate the validity and analyze the accuracy of our methodology through a comprehensive experimental study using commercially available technology, namely TelosB motes running TinyOS.

On the capacity of cluster-tree ZigBee networks

Modeling the fundamental performance limits of Wireless Sensor Networks (WSNs) is of paramount importance to understand their behavior under worst-case conditions and to make the appropriate design choices. In that direction this paper contributes with an analytical methodology for modeling cluster-tree WSNs where the data sink can either be static or mobile. We assess the validity and pessimism of analytical model by comparing the worst-case results with the values measured through an experimental test-bed based on Commercial-Off- The-Shelf (COTS) technologies, namely TelosB motes running TinyOS.

On a reliable handoff procedure for supporting mobility in wireless sensor networks

Wireless sensor network (WSN) applications such as patients’ health monitoring in hospitals, location-aware ambient intelligence, industrial monitoring /maintenance or homeland security require the support of mobile nodes or node groups. In many of these applications, the lack of network connectivity is not admissible or should at least be time bounded, i.e. mobile nodes cannot be disconnected from the rest of the WSN for an undefined period of time. In this context, we aim at reliable and real-time mobility support in WSNs, for which appropriate handoff and rerouting decisions are mandatory. This paper1 drafts a mechanism and correspondent heuristics for taking reliable handoff decisions in WSNs. Fuzzy logic is used to incorporate the inherent imprecision and uncertainty of the physical quantities at stake.

Real-time communications over wired/wireless PROFIBUS networks supporting inter-cell mobility

PROFIBUS is an international standard (IEC 61158, EN 50170) for factory-floor communications, with several thousands of installations worldwide. Taking into account the increasing need for mobile devices in industrial environments, one obvious solution is to extend traditional wired PROFIBUS networks with wireless capabilities. In this paper, we outline the major aspects of a hybrid wired/wireless PROFIBUS-based architecture, where most of the design options were made in order to guarantee the real-time behaviour of the overall network. We also introduce the timing unpredictability problems resulting from the co-existence of heterogeneous physical media in the same network. However, the major focus of this paper is on how to guarantee real-time communications in such a hybrid network, where nodes (and whole segments) can move between different radio cells (inter-cell mobility). Assuming a simple mobility management mechanism based on mobile nodes performing periodic radio channel assessment and switching, we propose a methodology to compute values for specific parameters that enable an optimal (minimum) and bounded duration of the handoff procedure.

Mobile collaborative cloudless computing

Although the computational power of mobile devices has been increasing, it is still not enough for some classes of applications. In the present, these applications delegate the computing power burden on servers located on the Internet. This model assumes an always-on Internet connectivity and implies a non-negligible latency. The thesis addresses the challenges and contributions posed to the application of a mobile collaborative computing environment concept to wireless networks. The goal is to define a reference architecture for high performance mobile applications. Current work is focused on efficient data dissemination on a highly transitive environment, suitable to many mobile applications and also to the reputation and incentive system available on this mobile collaborative computing environment. For this we are improving our already published reputation/incentive algorithm with knowledge from the usage pattern from the eduroam wireless network in the Lisbon area.

Extending access to remote labs from mobile devices in educational contexts

This paper describes how to extend the access to remote experiments from mobile devices, aiming to better engage digital native students who expect a more interactive and ubiquitous access mode. The extension is based on features of HTML5 and the jQuery Mobile framework, which allow accessing the experiments from different operating systems via the browser or native applications. As a result, users have a richer interaction mode with the experiments, which includes access from simple hand-held devices such as smartphones and PDAs. Extending the access to remote experiments, from simple devices, enables its use in other educational stages, such as high schools, where teachers struggle to engage students in STEM learning. By enabling students to use their everyday "technological companions", e.g. cellular phones, to access remote experiments, we seek to increase the educational value of this technology-enhanced learning resource.

Mining social individuals movements and friends based on mobile devices

Trabalho de Projeto realizado para obtenção do grau de Mestre em Engenharia Informática e de Computadores