This thesis describes the design of a Virtual Application Networking Infrastructure (VANI) node that can be used to facilitate network architecture experimentation. Cur- rently the VANI nodes provide four classes of physical resources – processing, reconfig- urable hardware, storage and interconnection fabric – but the set of sharable resources can be expanded. Virtualization software allows slices of these resources to be appor- tioned to VANI nodes that can in turn be interconnected to form virtual networks, which can operate according to experimental network and application protocols. This thesis discusses the design decisions that have been made in the development of this system and provides a detailed description of the prototype, including how users interact with the resources and the interfaces provided by the virtualization layers.

DNA sequence assembly is one of the fundamental areas of bioinformatics. It involves the correct formation of a genome sequence from its DNA fragments ("reads") by aligning and merging the fragments. There are different sequencing technologies -- some support long DNA reads and the others, shorter DNA reads. There are sequence assembly programs specifically designed for these different types of raw sequencing data.<p> This work explores and experiments with these different types of assembly software in order to compare their performance on the type of data for which they were designed, as well as their performance on data for which they were not designed, and on mixed data. Such results are useful for establishing good procedures and tools for sequence assembly in the current genomic environment where read data of different lengths are available. This work also investigates the effect of the presence or absence of quality information on the results produced by sequence assemblers.<p> Five strategies were used in this research for assembling mixed data sets and the testing was done using a collection of real and artificial data sets for six bacterial organisms. The results show that there is a broad range in the ability of some DNA sequence assemblers to handle data from various sequencing technologies, especially data other than the kind they were designed for. For example, the long-read assemblers PHRAP and MIRA produced good results from assembling 454 data. The results also show the importance of having an effective methodology for assembling mixed data sets. It was found that combining contiguous sequences obtained from short-read assemblers with long DNA reads, and then assembling this combination using long-read assemblers was the most appropriate approach for assembling mixed short and long reads. It was found that the results from assembling the mixed data sets were better than the results obtained from separately assembling individual data from the different sequencing technologies. DNA sequence assemblers which do not depend on the availability of quality information were used to test the effect of the presence of quality values when assembling data. The results show that regardless of the availability of quality information, good results were produced in most of the assemblies.<p> In more general terms, this work shows that the approach or methodology used to assemble DNA sequences from mixed data sources makes a lot of difference in the type of results obtained, and that a good choice of methodology can help reduce the amount of effort spent on a DNA sequence assembly project.

The Department of Energy (DOE) Nuclear Energy Research Initiative (NERI) Direct Energy Conversion project has identified the fission fragment magnetic collimator reactor (FFMCR) as a promising direct fission fragment conversion concept. The US DOE NERI Proof-of-Principle Project at Texas A&M is focused on experimental verification of FFMCR operation principles. The purpose of this experiment was to test design parameters of a scaled prototype of a direct energy collector chamber of the FFMCR. The charge collection efficiency was found using a He+ ion beam to be approximately 88% for beam energies ranging from 20 to 80 keV. The 2.4 10^12 ± 10% ohm resistor used in the experiment holds-up under the stress of high voltage to 40 kV. Electric current leakage tests of the charge collection device also indicate that Teflon® is quite sufficient as an insulator for potentials as high as 40 kV. It is suggested that the present work be extended to determine power efficiencies and to achieve results with higher beam energies.

Specific and sensitive recognition of foreign agents is a critical attribute of the overall effective immune system required for maintaining host protection against challenge from pathogenic cells. In the humoral arm of the immune system, this recognition attribute is carried out by the cell surface bound immunoglobulin-like receptors (BCR) and its soluble forms i.e. antibodies. Over several million years of evolution, the immune system has adopted several strategies for diversifying the antibody sequence and thus its ability to recognize an astronomical variety of molecules through the combinatorial assembly of a small number of DNA segments or genes. Among these immunoglobulin gene diversification strategies, antibody somatic VDJ recombination and junctional diversity are the fundamental mechanisms in generating a broad range of antibody specificities. Understanding how the genetic diversity of antibodies is affected in health and disease is critical for a wide range of medical applications, from vaccine evaluation to diagnostics and therapeutics discovery. Because of the very large number of distinct antibodies encoded by the more than 100 billion B cells in humans, it is essential to use high throughput next generation sequencing technologies in order to obtain an adequate sampling of the sequences and relative abundance of different antibodies expressed by B cells in clinical samples. The process requires rigorous methods for first, experimentally determining the sequences of antibodies in a sample and for second, informatics tools designed for distilling this information for practical purposes. This dissertation describes a variety of experimental approaches and informatics tools developed for the determination and mining of the antibody repertoire. The information from this work has led to major conclusions regarding the nature of the antibody repertoire in healthy individuals, in volunteers following vaccination, and in HIV-1 patients. / text

ITC/USA 2014 Conference Proceedings / The Fiftieth Annual International Telemetering Conference and Technical Exhibition / October 20-23, 2014 / Town and Country Resort & Convention Center, San Diego, CA / There is a need for a capability that enables setup and execution of tests, including integration of new instrumentation into the T&E range environment more rapidly and reliably than with existing methods, and with reduced cost and effort. Moreover, because individual ranges have developed approaches to range control and data distribution which are often range-specific and which call for significant interface development when integrating new instrumentation and systems to the range environment, there is a need to develop a range control and data distribution mechanism that can be reused throughout the T&E community. The purpose of the Next Generation Range Control and Data Distribution (NGRC&DD) project, which is funded by the Test Resource Management Center's (TRMC) Central Test and Evaluation Investment Program (CTEIP), is to develop a capability that modernizes and enhances system control and data distribution in DoD ranges. The Test and Training Enabling Architecture (TENA) is an underlying technology used by NGRC&DD. Migrating to the TENA middleware requires a fundamental reexamination of what data is produced and how it is distributed. TENA offers some tools and mechanisms for ranges that are advantageous relative to traditional methods of data dissemination as well as other versions of middleware available to the community.

A dominant ENU screen produced mouse line 7238 with large platelets. Sequence capture and Next Generation sequencing identified a mutation in Myh9 at Q1443L [1]. Mice were tested for aspects of MYH9-Related Disease (MYH9RD), a rare human condition caused by mutations within MYH9; macrothrombocytopenia and neutrophil inclusions are found in almost all cases, while deafness, cataracts and renal disease have variable penetrance and severity. Myh9Q1443L/+ and Myh9Q1443L/Q1443L animals have neutrophil inclusions [1] and increased cataracts at 2, 6 and 12 months; Myh9Q1443L/Q1443L animals at 12 months have changes in kidney output [2]. Immunofluoresence showed changes in protein expression in glomeruli at two months. This is the first ENU mouse model identified by a sequence capture mechanism, and the first mouse line to produce a point mutation within the Myh9 gene [1,2]. This mouse models MYH9RD, and is an invaluable tool to understand the role of this protein, and to determine mechanisms underlying this disease.

A dominant ENU screen produced mouse line 7238 with large platelets. Sequence capture and Next Generation sequencing identified a mutation in Myh9 at Q1443L [1]. Mice were tested for aspects of MYH9-Related Disease (MYH9RD), a rare human condition caused by mutations within MYH9; macrothrombocytopenia and neutrophil inclusions are found in almost all cases, while deafness, cataracts and renal disease have variable penetrance and severity. Myh9Q1443L/+ and Myh9Q1443L/Q1443L animals have neutrophil inclusions [1] and increased cataracts at 2, 6 and 12 months; Myh9Q1443L/Q1443L animals at 12 months have changes in kidney output [2]. Immunofluoresence showed changes in protein expression in glomeruli at two months. This is the first ENU mouse model identified by a sequence capture mechanism, and the first mouse line to produce a point mutation within the Myh9 gene [1,2]. This mouse models MYH9RD, and is an invaluable tool to understand the role of this protein, and to determine mechanisms underlying this disease.

No description available.

Water sources are susceptible to faecal contamination from animal and human pollution sources. Pollution of our waterways has significant implications on human health, especially from a pathogen perspective. Microbial source tracking (MST) is a promising field which aims to identify the sources of faecal contamination, and thereby allowing for the development of effective management strategies to minimise pollution and the impact on human health. Many of the currently used methods rely on the identification of host-specific markers within the 16S ribosomal RNA (rRNA) gene of bacteria by use of amplification techniques such as polymerase chain reaction (PCR). However, these methods can be limited by sensitivity, quantification, geographical differences and issues of cost which can limit how many markers are evaluated. Developments in DNA sequencing technologies over the past decade have led to a number of next generation sequencing (NGS) platforms which have a rapid, high throughput approach, resulting in an exponential decrease in the cost of sequencing. This has enabled the development of sequence-based metagenomics, where entire communities from environmental samples can be analysed based on their genetic material. The ability to barcode allows for analysis of multiple samples at once, reducing the cost of sequencing environmental samples even further. This is a promising technique for MST, which has had little investigation to date. The primary focus of the studies described in this thesis was to evaluate the use of NGS technology through a metagenomic approach. Roche 454 amplicon sequencing was used to sequence a 16S rRNA gene target, amplified from faecal and water samples from various sources in New Zealand. Barcode strategies were incorporated in the amplification design to allow multiple samples to be sequenced simultaneously. A proof-of-concept study initially utilised a small sequence dataset to evaluate a range of analysis tools available. Taxonomic identification and diversity measures were used to evaluate a selection of currently available tools designed for analysing metagenomic data, with the Quantitative Insights Into Microbial Ecology (QIIME) platform decided upon for further studies. A larger study, including 35 faecal samples from 13 difference sources and 10 water samples, resulted in 522,065 raw sequencing reads. Diversity results suggest three phyla, Bacteroidetes, Firmicutes and Proteobacteria, are strongly represented across all faecal sources analysed. Microbial diversity analysis using clustering techniques provided evidence of host source being the largest influence on bacterial diversity, with samples from each source generally clustering together. This technique could not be used to identify sources of contamination sources in water samples as the water samples all clustered separately from the faecal samples. More successful was the use of taxonomic classifications to determine bacteria genera that were potentially specific to one source. Water samples were screened for these genera, with six out of the ten water samples being indicators of either ruminant or human contamination. Faecal and water samples were also analysed for a selection of published 16S rRNA PCR markers, using a computational motif-based search method. Of the twenty motifs screened for, 14 were found to be relatively source-specific for ruminant, human, dog or pig faecal samples, with some cross-reactivity with chicken and possum samples. Using this method, the contamination source for six of the ten water samples was identified, with the remaining four samples found to not have enough sequences to assess with confidence. Both metagenomic strategies produced comparable results which were consistent with previous MST analysis. This project demonstrates the potential application of next generation sequencing technologies to microbial source tracking, suggesting the possibility this approach to replace existing microbial source tracking methods.

Το περιεχόμενο του συγκράματος ασχολείται με τη μελέτη αρχιτεκτονικών διαστρωμάτωσης για τη διερεύνηση των λειτουργικών απαιτήσεων των ασύρματων δικτύων επόμενης γενιάς. Αφού γίνει η μελέτη των τεχνικών καταχώρισης συχνοτήτων στα κυτταρικά συστήματα των κινητών επικοινωνιών κατόπιν αναλύονται οι λειτουργικές διαδικασίες των κυτταρικών συστημάτων κινητής τηλεφωνίας όπως και το μοντέλο καταχώρισης ραδιοπόρων το οποίο βασίζεται στις τεχνικές Erlang. Ακολούθως προτείνονται μέσω μαθηματικής ανάλυσης διεπίπεδες τεχνικές μεταγωγής. Εν συνεχεία, παρουσιάζεται η εφαρμογή της πολυεπίπεδης αρχιτεκτονικής στα σύγχρονα κυτταρικά συστήματα όπου αναλύεται η αρχιτεκτονική UMTS/HAP. Στα αποτελέσματα της προσομοίωσης που κάνουμε στο σύστημα μας, παρατηρούμε την αισθητή μείωση της dropping/blocking πιθανότητας όταν εφαρμοστεί η προτεινόμενη τεχνική. / The subject of diploma is about studying architectures of multilayrer in next generation wireless networks. After we study registration techniques in cellar systems of wireless communication systems, we analyze operating processes of mobile network and sources registration based on Erlang's techniques. after all, it is presented the application of multilayer architecture in modern cell systems where architecture UNTS/HAP is analyzed. In the results of our simulation we see that the blocking/dropping probability is decreased when out technique is enabled