The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.

Integrative analysis of 111 reference human epigenomes

All one needs to know about fog computing and related edge computing paradigms: A complete survey

Recent emphasis on green communications has generated great interest in the investigations of energy harvesting communications and networking. Energy harvesting from ambient energy sources can potentially reduce the dependence on the supply of grid or battery energy, providing many attractive benefits to the environment and deployment. However, unlike the conventional stable energy, the intermittent and random nature of the renewable energy makes it challenging in the realization of energy harvesting transmission schemes. Extensive research studies have been carried out in recent years to address this inherent challenge from several aspects: energy sources and models, energy harvesting and usage protocols, energy scheduling and optimization, implementation of energy harvesting in cooperative, cognitive radio, multiuser and cellular networks, etc. However, there has not been a comprehensive survey to lay out the complete picture of recent advances and future directions. To fill such a gap, in this paper, we present an overview of the past and recent developments in these areas and highlight a number of possible future research avenues.

/pdf/advances-in-energy-harvesting-communications-past-present-3oubbkeycy.pdf

Advances in Energy Harvesting Communications: Past, Present, and Future Challenges

Wireless sensor networks (WSNs) research has pre-dominantly assumed the use of a portable and limited energy source, viz. batteries, to power sensors. Without energy, a sensor is essentially useless and cannot contribute to the utility of the network as a whole. Consequently, substantial research efforts have been spent on designing energy-efficient networking protocols to maximize the lifetime of WSNs. However, there are emerging WSN applications where sensors are required to operate for much longer durations (like years or even decades) after they are deployed. Examples include in-situ environmental/habitat monitoring and structural health monitoring of critical infrastructures and buildings, where batteries are hard (or impossible) to replace/recharge. Lately, an alternative to powering WSNs is being actively studied, which is to convert the ambient energy from the environment into electricity to power the sensor nodes. While renewable energy technology is not new (e.g., solar and wind) the systems in use are far too large for WSNs. Those small enough for use in wireless sensors are most likely able to provide only enough energy to power sensors sporadically and not continuously. Sensor nodes need to exploit the sporadic availability of energy to quickly sense and transmit the data. This paper surveys related research and discusses the challenges of designing networking protocols for such WSNs powered by ambient energy harvesting.

/pdf/wireless-sensor-networks-powered-by-ambient-energy-190hpq37ui.pdf

Wireless sensor networks powered by ambient energy harvesting (WSN-HEAP) - Survey and challenges

Survivability, the ability of a network to withstand and recover from failures, is one of the most important requirements of networks. Its importance is magnified in fiber optic networks with throughputs on the order of gigabits and terabits per second. This article takes a look at the techniques used to achieve survivability in traditional optical networks, and how those techniques are evolving to make next-generation WDM networks survivable.

Survivability in optical networks

The design of survivable all-optical networks based on self-healing WDM rings (SHR/WDM) to provide 100% protection from any single link failure requires the joint solution of three sub-problems. These are the ring cover of the mesh topology (the RC sub-problem), the routing of working lightpaths between node pairs to support traffic demands (the WL sub-problem) and the selection of the SHR/WDM spare wavelengths for the protection of every link traffic (the SW subproblem). This paper presents an integer linear programming (ILP) formulation of the problem of minimizing the total wavelength mileage (/spl lambda/-miles) required to support a set of given traffic demands in a given network topology using SHR/WDM employing 1:N line protection mechanism (the WRL problem). This formulation allows to jointly and optimally solve the three subproblems, and yields up to 15% reduction of the total /spl lambda/-miles required by existing solutions that separately resolve the sub-problems. A simplified sub-optimal solution of the WRL problem is also provided, that yields results few percent worse than the optimal solution and that is tractable for networks whose size is on the order of the pan-European network, i.e., 19 nodes.

Survivable networks based on optimal routing and WDM self-healing rings

One class of wireless sensor networks makes use of sensor nodes that recharge their batteries by harvesting energy from the surrounding environment. Being continuously recharged, the battery does not need to be replaced regularly and the sensor node is maintenance-free. A key module in such sensor network solutions is the data link automatic repeat request (ARQ) protocol, which must be designed to reliably deliver sensor nodes data at the minimum energy cost. With this objective in mind, two ARQ protocol classes are compared. In one class, each sensor node operates individually. In the other, the concept of cooperative communications is adopted, whereby neighboring sensor nodes help each other during the retransmission process. It is shown that the use of cooperative ARQ protocols in energy harvesting sensor networks enables sensor nodes to balance their energy consumption to match their own battery recharge rate. In turn, a balanced energy consumption-to-recharge rate ratio has the potential to improve the network throughput. Both classes of ARQ protocols are analyzed and compared. Estimated throughput gains are discussed under various network scenarios.

/pdf/cooperative-and-reliable-arq-protocols-for-energy-harvesting-4yyo8mjo0n.pdf

Cooperative and Reliable ARQ Protocols for Energy Harvesting Wireless Sensor Nodes

This paper presents both theoretical and experimental studies carried on wavelength-division multiplexing (WDM) networks with arbitrary (mesh) topology that provide optical circuits with differentiated reliability (DiR). Reliability is obtained by means of a modified shared path protection (SPP) switching scheme-here referred to as SPP-DiR. As explained in the paper, SPP-DiR networks provide multiple degrees of circuit reliability that satisfy client-specific reliability requirements in a cost-effective way. The theoretical study first defines the problem of optimally designing SPP-DiR WDM networks. It then presents a time-efficient suboptimal algorithm that determines the routing and the reliability degree of each demand in the given traffic matrix by applying both the conventional SPP and the SPP-DiR scheme. When compared to dedicated path protection switching, results obtained for the pan-European network using the proposed algorithm indicate cost reductions of about 16% when SPP is applied, and up to 34% when SPP-DiR is applied. The experimental study describes the /spl Omega/ testbed-a WDM optical circuit-switched mesh network with an IP control plane-which is believed to be the first testbed ever built that makes use of the SPP-DiR scheme. Experimental results performed on the /spl Omega/ testbed report restoration times of the optical circuits-disrupted by a fiber fault-that are few tens of milliseconds.

Differentiated reliability in optical networks: theoretical and practical results

The authors (Fumagalli and Tacca (2001)) introduced the concept of differentiated reliability (DiR) applied to dedicated path protection (DPP) switching in wavelength division multiplexing (WDM) rings. By means of the DiR concept, a network can be designed to provide multiple degrees of reliability and efficiently satisfy the user-specific requirements, yet minimizing the network total cost. This paper extends the DiR concept to the case of shared path protection (SPP) switching in arbitrary (mesh) topology, the so called SPP-DiR. A time efficient algorithm is proposed to determine the primary and backup path of each demand in both conventional SPP and SPP-DiR (WDM) networks. When compared to DPP, results obtained for the pan-European network by using the proposed algorithm indicate cost reductions of about 16% when SPP is applied, and up to 34% when SPP-DiR is applied.

Shared path protection with differentiated reliability

The concept of differentiated reliability, (DiR) was recently introduced by the authors to provide multiple reliability degrees (or classes) at the same network layer using a common protection mechanism, e.g., path switching. According to the DiR concept, each connection at the layer under consideration is guaranteed a minimum reliability degree, defined as the maximum failure probability allowed for that connection. The reliability degree chosen for a given connection is thus determined by the application requirements, and not by the actual network topology, design constraints, robustness of the network components, and span of the connection. In the paper the DiR concept is applied to designing the wavelength division multiplexing (WDM) layer of a ring network in which wavelength conversion is not available. To solve the routing and wavelength assignment problem at the WDM layer an efficient algorithm is proposed that resorts to reusable protection wavelengths while guaranteeing the required reliability degree of each connection. Lower bounds on the network bandwidth required by two approaches-respectively based on non-reusable and reusable protection wavelengths-reveal interesting properties of the DiR concept and the proposed algorithm.

Marco Tacca

Papers

Survivable networks based on optimal routing and WDM self-healing rings

Cooperative and Reliable ARQ Protocols for Energy Harvesting Wireless Sensor Nodes

Differentiated reliability in optical networks: theoretical and practical results

Shared path protection with differentiated reliability

Differentiated reliability (DiR) in WDM rings without wavelength converters