DEVELOPMENT OF NOVEL METHODS TO MINIMIZE THE IMPACT OF SEQUENCING ERRORS IN THE NEXT-GENERATION SEQUENCING DATA ANALYSIS

Next-generation sequencing (NGS) technology has become a prominent tool in biological and biomedical research. However, NGS data analysis, such as de novo assembly, mapping and variants detection is far from maturity, and the high sequencing error-rate is one of the major problems. . To minimize the impact of sequencing errors, we developed a highly robust and efficient method, MTM, to correct the errors in NGS reads. We demonstrated the effectiveness of MTM on both single-cell data with highly non-uniform coverage and normal data with uniformly high coverage, reflecting that MTM’s performance does not rely on the coverage of the sequencing reads. MTM was also compared with Hammer and Quake, the best methods for correcting non-uniform and uniform data respectively. For non-uniform data, MTM outperformed both Hammer and Quake. For uniform data, MTM showed better performance than Quake and comparable results to Hammer. By making better error correction with MTM, the quality of downstream analysis, such as mapping and SNP detection, was improved. SNP calling is a major application of NGS technologies. However, the existence of sequencing errors complicates this process, especially for the low coverage (

Diversity of zooplankton assemblages at Station L4, Western English Channel, measured using next generation DNA sequencing

Background: Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel Next Generation Sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify the richness and diversity of a mixed zooplankton assemblage from a productive monitoring site in the Western English Channel. Methodology/Principle Findings: Plankton WP2 replicate net hauls (200 µm) were taken at the Western Channel Observatory long-term monitoring station L4 in September 2010 and January 2011. These samples were analysed by microscopy and metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene using the 454 pyrosequencing platform. Following quality control a total of 419,042 sequences were obtained for all samples. The sequences clustered in to 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 138 OTUs to species level, 11 to genus level and 1 to order, <2.5% of sequences were classified as unknowns. By comparison a skilled microscopic analyst was able to routinely enumerate only 75 taxonomic groups. Conclusions: The percentage of OTUs assigned to major eukaryotic taxonomic groups broadly aligns between the metagenetic and morphological analysis and are dominated by Copepoda. However, the metagenetics reveals a previously hidden taxonomic richness, especially for Copepoda and meroplankton such as Bivalvia, Gastropoda and Polychaeta. It also reveals rare species and parasites. We conclude that Next Generation Sequencing of 18S amplicons is a powerful tool for estimating diversity and species richness of zooplankton communities.

Blogs: On the Cutting Edge of the Next-generation Web

This article analyses a number of social and cultural aspects of the blog phenomenon with the methodological aid of a complexity model, the New Techno-social Environment (hereinafter also referred to by its Spanish acronym, NET, or Nuevo Entorno Tecnosocial) together with the socio-technical approach of the two blogologist authors. Both authors are researchers interested in the new reality of the Digital Universal Network (DUN). After a review of some basic definitions, the article moves on to highlight some key characteristics of an emerging blog culture and relates them to the properties of the NET. Then, after a brief practical parenthesis for people entering the blogosphere for the first time, we present some reflections on blogs as an evolution of virtual communities and on the changes experienced by the inhabitants of the infocity emerging from within the NET. The article concludes with a somewhat disturbing question; whether among these changes there might not be a gradual transformation of the structure and form of human intelligence.

Public support for the deployment of next generation access networks-Common themes, methodological caveats and further research

Next generation telecommunications infrastructures are considered as a principal example of a new technology for sustainable economic growth. From their deployment it is expected that a wealth of innovations – hopefully converted into economic growth – new sources of employment and improved quality of life will result. In line with these prospects, public administrations at supranational, national, regional and local levels have encouraged the development of these new infrastructures. Moreover, in times of economic crisis, public assistance to deploy such networks encompasses the promise of placing a weak economy on the road to prosperity. However, such arguments and political claims clearly require rigorous assessment. In particular, any such assessment must adequately address the appropriate form of modelling that best captures key elements for identifiable progress from next generation access networks (NGAN).

Next Generation of Energy Residential Gateways for Demand Response and Dynamic Pricing

Predictions about electric energy needs, based on current electric energy models, forecast that the global energy consumption on Earth for 2050 will double present rates. Using distributed procedures for control and integration, the expected needs can be halved. Therefore implementation of Smart Grids is necessary. Interaction between final consumers and utilities is a key factor of future Smart Grids. This interaction is aimed to reach efficient and responsible energy consumption. Energy Residential Gateways (ERG) are new in-building devices that will govern the communication between user and utility and will control electric loads. Utilities will offer new services empowering residential customers to lower their electric bill. Some of these services are Smart Metering, Demand Response and Dynamic Pricing. This paper presents a practical development of an ERG for residential buildings.

An Analysis of Next Generation Access Networks Deployment in rural areas

Next generation access networks (NGAN) will support a renewed electronic communication market where main opportunities lie in the provision of ubiquitous broadband connectivity, applications and content. From their deployment it is expected a wealth of innovations. Within this framework, the project reviews the variety of NGAN deployment options available for rural environments, derives a simple method for approximate cost calculations, and then discusses and compares the results obtained. Data for Spain are used for practical calculations, but the model is applicable with minor modifications to most of the rural areas of European countries. The final part of the paper is devoted to review the techno-economic implications of a network deployment in a rural environment as well as the adequacy and possible developments of the regulatory framework involved

Which could be the role of Hybrid Fibre Coax in Next Generation Access networks?

Next generation access networks (NGAN) will support a renewed communication structure where opportunities lie in the provision of ubiquitous broadband connectivity, a wide variety of new applications, appealing contents and a general support to the sustainable growth of diverse sectors. From their deployment it is expected a wealth of innovations, jobs creation and a new wave of economic growth. In this paper we discuss which could be the role of Hybrid Fibre Coax (HFC) in the Next Generation Access Network (NGAN) roadmap. Thus, we propose a simplified model for making approximate cost calculations for HFC deployment based on the geographic and sociodemographic characteristics of Spain. Considering the latest evolution of HFC based on DOCSIS 3.0 from integrated (I-CMTS) towards modular (M-CMTS), the results from the model are compared with the most competitive NGAN for ultrabroadband speeds: Fibre to the Home (FTTH) based on Gigabitcapable Passive Optical Networks (GPON)

How much energy will your NGN consume? A model for energy consumption in next generation access networks: The case of Spain

The contribution to global energy consumption of the information and communications technology (ICT) sector has increased considerably in the last decade, along with its growing relevance to the overall economy. This trend will continue due to the seemingly ever greater use of these technologies, with broadband data traffic generated by the usage of telecommunication networks as a primary component. In fact, in response to user demand, the telecommunications industry is initiating the deployment of next generation networks (NGNs). However, energy consumption is mostly absent from the debate on these deployments, in spite of the potential impact on both expenses and sustainability. In addition, consumers are unaware of the energy impact of their choices in ultra-broadband services. This paper focuses on forecasting energy consumption in the access part of NGNs by modelling the combined effect of the deployment of two different ultra-broadband technologies (FTTH-GPON and LTE), the evolution of traffic per user, and the energy consumption in each of the networks and user devices. Conclusions are presented on the levels of energy consumption, their cost and the impact of different network design parameters. The effect of technological developments, techno-economic and policy decisions on energy consumption is highlighted. On the consumer side, practical figures and comparisons across technologies are provided. Although the paper focuses on Spain, the analysis can be extended to similar countries.

Implications of data-intensive applications for next generation mobile networks

Lately, the mobile data market has moved into a growth stage triggered by two facts: affordability of mobile broadband, and availability of data-friendly devices. At this stage, market growth is no longer dependent on push strategies from suppliers; on the contrary, demand is now driving the market. However, it will not be easy for mobile operating companies to cope up with the demand to come in the near future. The infrastructure that is needed to support corresponding demand is far from completion. Operators are forced to make heavy investments to upgrade and expand their networks. To decide how to handle the present and upcoming demand, they need to identify and understand the characteristics of the scenarios they face. This is precisely the aim of this article, which provides figures on the consequences for mobile infrastructures of a generalised mobile media uptake. Data from the Spanish mobile deployment case have been used to arrive at practical figures and illustration of results, but the conclusions are easily extended to other countries and regions

The growth of demand will limit output growth for food over the next quarter century

The rate of growth of world food demand will be much slower for 1990–2010 than it was for the prior three decades. The major factor determining the increase in food demand is population growth. Income growth has a much smaller effect. From 1960 to 1990, population growth accounted for approximately three fourths of the growth in demand or use of grain. For 1990–2010, it is anticipated that population growth will account for nearly all of the increase in world demand for grain. The rate of population growth from 1990 to 2020 is projected to be at an annual rate of 1.3% compared with 1.9% for 1960 to 1990—a decline of more than 30%. World per capita use of grain will increase very little—perhaps by 4%. The increase in grain use is projected to be 40% less than in 1960–1990. It is anticipated that real grain prices will decline during the period, although not nearly as much as the 40% decline in the previous three decades. Concern has been expressed concerning the deterioration of the quality and productivity of the world’s farmland. A study for China and Indonesia indicates that there has been no significant change in the productive capacity of the land over the past 50 years. Contrary to numerous claims, the depth of the topsoil has not changed, indicating that erosion has had little or no impact.

Camp, clan, and kin among the Cow Creek Seminole of Florida / by Alexander Spoehr, Assistant Curator, American Ethnology and Archaeology.

v.33:no.1(1941)

Vote of the Corporation continuing the salary of the President up to the next commencement,

This folder contains two nineteenth-century handwritten copies of the vote.