Proteins, drug targets and the mechanisms they control : the simple truth about complex networks

Realizing the promise of molecularly targeted inhibitors for cancer therapy will require a new level of knowledge about how a drug target is wired into the control circuitry of a complex cellular network. Here we review general homeostatic principles of cellular networks that enable the cell to be resilient in the face of molecular perturbations, while at the same time being sensitive to subtle input signals. Insights into such mechanisms may facilitate the development of combination therapies that take advantage of the cellular control circuitry, with the aim of achieving higher efficacy at a lower drug dosage and with a reduced probability of drug-resistance development.

Forewarding in Mobile Opportunistic Networks

Recent advances in processor speeds, mobile communications and battery life have enabled computers to evolve from completely wired to completely mobile. In the most extreme case, all nodes are mobile and communication takes place at available opportunities – using both traditional communication infrastructure as well as the mobility of intermediate nodes. These are mobile opportunistic networks. Data communication in such networks is a difficult problem, because of the dynamic underlying topology, the scarcity of network resources and the lack of global information. Establishing end-to-end routes in such networks is usually not feasible. Instead a store-and-carry forwarding paradigm is better suited for such networks. This dissertation describes and analyzes algorithms for forwarding of messages in such networks. In order to design effective forwarding algorithms for mobile opportunistic networks, we start by first building an understanding of the set of all paths between nodes, which represent the available opportunities for any forwarding algorithm. Relying on real measurements, we enumerate paths between nodes and uncover what we refer to as the path explosion effect. The term path explosion refers to the fact that the number of paths between a randomly selected pair of nodes increases exponentially with time. We draw from the theory of epidemics to model and explain the path explosion effect. This is the first contribution of the thesis, and is a key observation that underlies subsequent results. Our second contribution is the study of forwarding algorithms. For this, we rely on trace driven simulations of different algorithms that span a range of design dimensions. We compare the performance (success rate and average delay) of these algorithms. We make the surprising observation that most algorithms we consider have roughly similar performance. We explain this result in light of the path explosion phenomenon. While the performance of most algorithms we studied was roughly the same, these algorithms differed in terms of cost. This prompted us to focus on designing algorithms with the explicit intent of reducing costs. For this, we cast the problem of forwarding as an optimal stopping problem. Our third main contribution is the design of strategies based on optimal stopping principles which we refer to as Delegation schemes. Our analysis shows that using a delegation scheme reduces cost over naive forwarding by a factor of O(√N), where N is the number of nodes in the network. We further validate this result on real traces, where the cost reduction observed is even greater. Our results so far include a key assumption, which is unbounded buffers on nodes. Next, we relax this assumption, so that the problem shifts to one of prioritization of messages for transmission and dropping. Our fourth contribution is the study of message prioritization schemes, combined with forwarding. Our main result is that one achieves higher performance by assigning higher priorities to young messages in the network. We again interpret this result in light of the path explosion effect.

Methodologies for traffic profiling in communication networks

Internet Tra c, Internet Applications, Internet Attacks, Tra c Pro ling, Multi-Scale Analysis abstract Nowadays, the Internet can be seen as an ever-changing platform where new and di erent types of services and applications are constantly emerging. In fact, many of the existing dominant applications, such as social networks, have appeared recently, being rapidly adopted by the user community. All these new applications required the implementation of novel communication protocols that present di erent network requirements, according to the service they deploy. All this diversity and novelty has lead to an increasing need of accurately pro ling Internet users, by mapping their tra c to the originating application, in order to improve many network management tasks such as resources optimization, network performance, service personalization and security. However, accurately mapping tra c to its originating application is a di cult task due to the inherent complexity of existing network protocols and to several restrictions that prevent the analysis of the contents of the generated tra c. In fact, many technologies, such as tra c encryption, are widely deployed to assure and protect the con dentiality and integrity of communications over the Internet. On the other hand, many legal constraints also forbid the analysis of the clients' tra c in order to protect their con dentiality and privacy. Consequently, novel tra c discrimination methodologies are necessary for an accurate tra c classi cation and user pro ling. This thesis proposes several identi cation methodologies for an accurate Internet tra c pro ling while coping with the di erent mentioned restrictions and with the existing encryption techniques. By analyzing the several frequency components present in the captured tra c and inferring the presence of the di erent network and user related events, the proposed approaches are able to create a pro le for each one of the analyzed Internet applications. The use of several probabilistic models will allow the accurate association of the analyzed tra c to the corresponding application. Several enhancements will also be proposed in order to allow the identi cation of hidden illicit patterns and the real-time classi cation of captured tra c. In addition, a new network management paradigm for wired and wireless networks will be proposed. The analysis of the layer 2 tra c metrics and the di erent frequency components that are present in the captured tra c allows an e cient user pro ling in terms of the used web-application. Finally, some usage scenarios for these methodologies will be presented and discussed.

Wireless networks congestion control

Congestion control in wireless networks is an important and open issue. Previous research has proven the poor performance of the Transport Control Protocol (TCP) in such networks. The factors that contribute to the poor performance of TCP in wireless environments concern its unsuitability to identify/detect and react properly to network events, its TCP window based ow control algorithm that is not suitable for the wireless channel, and the congestion collapse due to mobility. New rate based mechanisms have been proposed to mitigate TCP performance in wired and wireless networks. However, these mechanisms also present poor performance, as they lack of suitable bandwidth estimation techniques for multi-hop wireless networks. It is thus important to improve congestion control performance in wireless networks, incorporating components that are suitable for wireless environments. A congestion control scheme which provides an e - cient and fair sharing of the underlying network capacity and available bandwidth among multiple competing applications is crucial to the definition of new e cient and fair congestion control schemes on wireless multi-hop networks. The Thesis is divided in three parts. First, we present a performance evaluation study of several congestion control protocols against TCP, in wireless mesh and ad-hoc networks. The obtained results show that rate based congestion control protocols need an eficient and accurate underlying available bandwidth estimation technique. The second part of the Thesis presents a new link capacity and available bandwidth estimation mechanism denoted as rt-Winf (real time wireless inference). The estimation is performed in real-time and without the need to intrusively inject packets in the network. Simulation results show that rt-Winf obtains the available bandwidth and capacity estimation with accuracy and without introducing overhead trafic in the network. The third part of the Thesis proposes the development of new congestion control mechanisms to address the congestion control problems of wireless networks. These congestion control mechanisms use cross layer information, obtained by rt-Winf, to accurately and eficiently estimate the available bandwidth and the path capacity over a wireless network path. Evaluation of these new proposed mechanisms, through ns-2 simulations, shows that the cooperation between rt-Winf and the congestion control algorithms is able to significantly increase congestion control eficiency and network performance.

Evaluation of the H.264 scalable video coding in error prone IP networks

The Joint Video Team, composed by the ISO/IEC Moving Picture Experts Group (MPEG) and the ITU-T Video Coding Experts Group (VCEG), has standardized a scalable extension of the H.264/AVC video coding standard called Scalable Video Coding (SVC). H.264/SVC provides scalable video streams which are composed by a base layer and one or more enhancement layers. Enhancement layers may improve the temporal, the spatial or the signal-to-noise ratio resolutions of the content represented by the lower layers. One of the applications, of this standard is related to video transmission in both wired and wireless communication systems, and it is therefore important to analyze in which way packet losses contribute to the degradation of quality, and which mechanisms could be used to improve that quality. This paper provides an analysis and evaluation of H.264/SVC in error prone environments, quantifying the degradation caused by packet losses in the decoded video. It also proposes and analyzes the consequences of QoS-based discarding of packets through different marking solutions.

Engineering PROFIBUS networks with heterogeneous transmission media

A significant number of process control and factory automation systems use PROFIBUS as the underlying fieldbus communication network. The process of properly setting up a PROFIBUS network is not a straightforward task. In fact, a number of network parameters must be set for guaranteeing the required levels of timeliness and dependability. Engineering PROFIBUS networks is even more subtle when the network includes various physical segments exhibiting heterogeneous specifications, such as bus speed or frame formats, just to mention a few. In this paper we provide underlying theory and a methodology to guarantee the proper operation of such type of heterogeneous PROFIBUS networks. We additionally show how the methodology can be applied to the practical case of PROFIBUS networks containing simultaneously DP (Decentralised Periphery) and PA (Process Automation) segments, two of the most used commercial-off-the-shelf (COTS) PROFIBUS solutions. The importance of the findings is however not limited to this case. The proposed methodology can be generalised to cover other heterogeneous infrastructures. Hybrid wired/wireless solutions are just an example for which an enormous eagerness exists.

A Management Tool for the Replication of Operating Systems in Wireless Communication Networks

To simplify computer management, various administration systems based on wired connections adopt advanced techniques to manage software configuration. Nevertheless, the strong relation between hardware and software makes for an individualism of that management, besides penalizing computational mobility and ubiquity. All these issues lead to degradation of scalability, flexibility and the facility to install and maintain distributed applications. This article presents an environment for centralized wireless communication network management, named WSE-OS (Wireless Sharing Environment - Operating Systems): a model based on Virtual Desktop Infrastructure (VDI) which associates virtualization techniques and safe remote access systems to create a distributed architecture as a base for a managing system. WSE-OS is capable of accomplishing the replication of operating system images using wireless communication network, besides offering abstraction of hardware to its clients, making the management more flexible and independent of wired connections. Results obtained from this work indicate that WSE-OS allows disseminating, through a single software configuration, the execution of data related to operating system images in client computers. WSE-OS can also be used as a management tool for operating systems in a wireless network.

Network node with wireless and wired interfaces: Nios II processor and uClinux to development of a NCAP embedded (IEEE 1451.1) with two interfaces, wireless (IEEE 1451.5) and wired (IEEE p1451.2)

This paper presents a NCAP embedded on DE2 kit with Nios II processor and uClinux to development of a network gateway with two interfaces, wireless (ZigBee) and wired (RS232) based on IEEE 1451. Both the communications, wireless and wired, were developed to be point-to-point and working with the same protocols, based on IEEE 1451.0-2007. The tests were made using a microcomputer, which through of browser was possible access the web page stored in the DE2 kit and send commands of control and monitoring to both TIMs (WTIM and STIM). The system describes a different form of development of the NCAP node to be applied in different environments with wired or wireless in the same node. © 2011 IEEE.

Design of a Wireless Vision Sensor for Object Tracking in Wireless Vision Sensor Networks

The integration of CMOS cameras with embedded processors and wireless communication devices has enabled the development of distributed wireless vision systems. Wireless Vision Sensor Networks (WVSNs), which consist of wirelessly connected embedded systems with vision and sensing capabilities, provide wide variety of application areas that have not been possible to realize with the wall-powered vision systems with wired links or scalar-data based wireless sensor networks. In this paper, the design of a middleware for a wireless vision sensor node is presented for the realization of WVSNs. The implemented wireless vision sensor node is tested through a simple vision application to study and analyze its capabilities, and determine the challenges in distributed vision applications through a wireless network of low-power embedded devices. The results of this paper highlight the practical concerns for the development of efficient image processing and communication solutions for WVSNs and emphasize the need for cross-layer solutions that unify these two so-far-independent research areas.

Fiber-Optic Technologies for Wireline and Wireless In-building Networks

This doctoral dissertation aims to establish fiber-optic technologies overcoming the limiting issues of data communications in indoor environments. Specific applications are broadband mobile distribution in different in-building scenarios and high-speed digital transmission over short-range wired optical systems. Two key enabling technologies are considered: Radio over Fiber (RoF) techniques over standard silica fibers for distributed antenna systems (DAS) and plastic optical fibers (POFs) for short-range communications. Hence, the objectives and achievements of this thesis are related to the application of RoF and POF technologies in different in-building scenarios. On one hand, a theoretical and experimental analysis combined with demonstration activities has been performed on cost-effective RoF systems. An extensive modeling on modal noise impact both on linear and non-linear characteristics of RoF link over silica multimode fiber has been performed to achieve link design rules for an optimum choice of the transmitter, receiver and launching technique. A successful transmission of Long Term Evolution (LTE) mobile signals on the resulting optimized RoF system over silica multimode fiber employing a Fabry-Perot LD, central launch technique and a photodiode with a built-in ball lens was demonstrated up to 525m with performances well compliant with standard requirements. On the other hand, digital signal processing techniques to overcome the bandwidth limitation of POF have been investigated. An uncoded net bit-rate of 5.15Gbit/s was obtained on a 50m long POF link employing an eye-safe transmitter, a silicon photodiode, and DMT modulation with bit and power loading algorithm. With the insertion of 3x2N quadrature amplitude modulation constellation formats, an uncoded net-bit-rate of 5.4Gbit/s was obtained on a 50 m long POF link employing an eye-safe transmitter and a silicon avalanche photodiode. Moreover, simultaneous transmission of baseband 2Gbit/s with DMT and 200Mbit/s with an ultra-wideband radio signal has been validated over a 50m long POF link.

Wireless Optical Communications for Intra-Spacecraft Networks Based on OCDMA with Random Optical Codes

In recent years, spacial agencies have shown a growing interest in optical wireless as an alternative to wired and radio-frequency communications. The use of these techniques for intra-spacecraft communications reduces the effect of take-off acceleration and vibrations on the systems by avoiding the need for rugged connectors and provides a significant mass reduction. Diffuse transmission also eases the design process as terminals can be placed almost anywhere without a tight planification to ensure the proper system behaviour. Previous studies have compared the performance of radio-frequency and infrared optical communications. In an intra-satellite environment optical techniques help reduce EMI related problems, and their main disadvantages - multipath dispersion and the need for line-of-sight - can be neglected due to the reduced cavity size. Channel studies demonstrate that the effect of the channel can be neglected in small environments if data bandwidth is lower than some hundreds of MHz.