Sequencing of 15 622 Gene-bearing BACs Clarifies the Gene-dense Regions of the Barley Genome

Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley–Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant

Cross-Platform Comparison of Untargeted and Targeted Lipidomics Approaches on Aging Mouse Plasma.

Lipidomics - the global assessment of lipids - can be performed using a variety of mass spectrometry (MS)-based approaches. However, choosing the optimal approach in terms of lipid coverage, robustness and throughput can be a challenging task. Here, we compare a novel targeted quantitative lipidomics platform known as the Lipidyzer to a conventional untargeted liquid chromatography (LC)-MS approach. We find that both platforms are efficient in profiling more than 300 lipids across 11 lipid classes in mouse plasma with precision and accuracy below 20% for most lipids. While the untargeted and targeted platforms detect similar numbers of lipids, the former identifies a broader range of lipid classes and can unambiguously identify all three fatty acids in triacylglycerols (TAG). Quantitative measurements from both approaches exhibit a median correlation coefficient (r) of 0.99 using a dilution series of deuterated internal standards and 0.71 using endogenous plasma lipids in the context of aging. Application of both platforms to plasma from aging mouse reveals similar changes in total lipid levels across all major lipid classes and in specific lipid species. Interestingly, TAG is the lipid class that exhibits the most changes with age, suggesting that TAG metabolism is particularly sensitive to the aging process in mice. Collectively, our data show that the Lipidyzer platform provides comprehensive profiling of the most prevalent lipids in plasma in a simple and automated manner

Traffic control mechanisms with cell rate simulation for ATM networks.

PhDAbstract not availabl

Quality of service optimization of multimedia traffic in mobile networks

Mobile communication systems have continued to evolve beyond the currently deployed Third Generation (3G) systems with the main goal of providing higher capacity. Systems beyond 3G are expected to cater for a wide variety of services such as speech, data, image transmission, video, as well as multimedia services consisting of a combination of these. With the air interface being the bottleneck in mobile networks, recent enhancing technologies such as the High Speed Downlink Packet Access (HSDPA), incorporate major changes to the radio access segment of 3G Universal Mobile Telecommunications System (UMTS). HSDPA introduces new features such as fast link adaptation mechanisms, fast packet scheduling, and physical layer retransmissions in the base stations, necessitating buffering of data at the air interface which presents a bottleneck to end-to-end communication. Hence, in order to provide end-to-end Quality of Service (QoS) guarantees to multimedia services in wireless networks such as HSDPA, efficient buffer management schemes are required at the air interface. The main objective of this thesis is to propose and evaluate solutions that will address the QoS optimization of multimedia traffic at the radio link interface of HSDPA systems. In the thesis, a novel queuing system known as the Time-Space Priority (TSP) scheme is proposed for multimedia traffic QoS control. TSP provides customized preferential treatment to the constituent flows in the multimedia traffic to suit their diverse QoS requirements. With TSP queuing, the real-time component of the multimedia traffic, being delay sensitive and loss tolerant, is given transmission priority; while the non-real-time component, being loss sensitive and delay tolerant, enjoys space priority. Hence, based on the TSP queuing paradigm, new buffer managementalgorithms are designed for joint QoS control of the diverse components in a multimedia session of the same HSDPA user. In the thesis, a TSP based buffer management algorithm known as the Enhanced Time Space Priority (E-TSP) is proposed for HSDPA. E-TSP incorporates flow control mechanisms to mitigate congestion in the air interface buffer of a user with multimedia session comprising real-time and non-real-time flows. Thus, E-TSP is designed to provide efficient network and radio resource utilization to improve end-to-end multimedia traffic performance. In order to allow real-time optimization of the QoS control between the real-time and non-real-time flows of the HSDPA multimedia session, another TSP based buffer management algorithm known as the Dynamic Time Space Priority (D-TSP) is proposed. D-TSP incorporates dynamic priority switching between the real-time and non-real-time flows. D-TSP is designed to allow optimum QoS trade-off between the flows whilst still guaranteeing the stringent real-time component’s QoS requirements. The thesis presents results of extensive performance studies undertaken via analytical modelling and dynamic network-level HSDPA simulations demonstrating the effectiveness of the proposed TSP queuing system and the TSP based buffer management schemes

Multimedia delivery in the future internet

The term “Networked Media” implies that all kinds of media including text, image, 3D graphics, audio and video are produced, distributed, shared, managed and consumed on-line through various networks, like the Internet, Fiber, WiFi, WiMAX, GPRS, 3G and so on, in a convergent manner [1]. This white paper is the contribution of the Media Delivery Platform (MDP) cluster and aims to cover the Networked challenges of the Networked Media in the transition to the Future of the Internet. Internet has evolved and changed the way we work and live. End users of the Internet have been confronted with a bewildering range of media, services and applications and of technological innovations concerning media formats, wireless networks, terminal types and capabilities. And there is little evidence that the pace of this innovation is slowing. Today, over one billion of users access the Internet on regular basis, more than 100 million users have downloaded at least one (multi)media file and over 47 millions of them do so regularly, searching in more than 160 Exabytes1 of content. In the near future these numbers are expected to exponentially rise. It is expected that the Internet content will be increased by at least a factor of 6, rising to more than 990 Exabytes before 2012, fuelled mainly by the users themselves. Moreover, it is envisaged that in a near- to mid-term future, the Internet will provide the means to share and distribute (new) multimedia content and services with superior quality and striking flexibility, in a trusted and personalized way, improving citizens’ quality of life, working conditions, edutainment and safety. In this evolving environment, new transport protocols, new multimedia encoding schemes, cross-layer inthe network adaptation, machine-to-machine communication (including RFIDs), rich 3D content as well as community networks and the use of peer-to-peer (P2P) overlays are expected to generate new models of interaction and cooperation, and be able to support enhanced perceived quality-of-experience (PQoE) and innovative applications “on the move”, like virtual collaboration environments, personalised services/ media, virtual sport groups, on-line gaming, edutainment. In this context, the interaction with content combined with interactive/multimedia search capabilities across distributed repositories, opportunistic P2P networks and the dynamic adaptation to the characteristics of diverse mobile terminals are expected to contribute towards such a vision. Based on work that has taken place in a number of EC co-funded projects, in Framework Program 6 (FP6) and Framework Program 7 (FP7), a group of experts and technology visionaries have voluntarily contributed in this white paper aiming to describe the status, the state-of-the art, the challenges and the way ahead in the area of Content Aware media delivery platforms