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Gatri, Aymen [Verfasser]. "Next Generation Optical Wireless Communication Systems : A Systems Approach / Aymen Gatri." Hamburg : disserta Verlag, 2019. http://d-nb.info/1199410845/34.
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Seung, Taehun. "Holistic-Lightweight Approach for actuation systems of the next generation aircraft." Universitätsverlag Chemnitz, 2017. https://monarch.qucosa.de/id/qucosa%3A34400.
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Currently the system development of aircraft engineering concentrates its focus on the reduction of energy consumption more than ever before. As a consequence, the efficiency of subsystems inside the aircraft is highlighted. According to previous investigations the simplification/unification of conventional multifaceted board energy systems by means of electric power management is the most promising way concerning aircraft global efficiency improvement.
The main aim of the present work was to optimize a multi-device, heavy duty EHA-System by introducing of a comprehensive perspective. In order to achieve the final, non-plus-ultra improvement level, the attributes of architecture, hardware and operation method were combined in an interactive manner, whereas particular attention has been paid to the mutual enhancing influences.
The maximum reduction of losses, the minimizing of consumption and weight optimization can be achieved concurrently when the physical coherences between the involved subsystems are understood and their hidden potentials are exploited.
This can only be achieved in one way and the detail follows: The most effective way to reduce both manufacturing effort and weight is to introduce a multiple-allocation philosophy. The highest reliability possible can be achieved by novel cascade-nested system architecture and strict restraining of the control logic. By employing an ultra-low-loss hardware concept, the energy efficiency can be maximized at a necessary minimum own weight. Last but not least, possibly the most important cognition is that an intelligent operation method will improve the actual system and influence the entire system positively and with a lower effort.
The final conclusion is that the only and reasonable way to achieve an ultimate optimized solution of an actuation system is an all-encompassing consideration. Eventually it was to recognize that the final result is nothing but ultimate lightweight architecture, i.e. a non-plus-ultra solution.Gegenwärtig konzentriert sich die Technologieentwicklung für Flugzeuge auf die Reduktion des Energieverbrauchs mehr denn je zuvor. Hierfür ist die Effizienz der an Bord befindlichen, nicht propulsiven Subsysteme neben der Wirkungsgradverbesserung der Triebwerke von zentraler Bedeutung. Laut vorangegangenen Untersuchungen und Studien ist die Vereinfachung bzw. Vereinheitlichung der Vielfalt der konventionellen Bordenergiesysteme durch ein adäquates Energiemanagement unter Verwendung von Elektrizität der aussichtsreichte Weg zur Effizienzverbesserung auf der Gesamtflugzeugebene. Durch die Elektrifizierung wurden die einzelnen Geräte zwar zuverlässiger und energieeffizienter als je zuvor aber gleichzeitig erheblich schwerer, sodaß ein signifikanter Verlust an Nutzlasten auf Gesamtflugzeugebene hervorgerufen wird. Das Hauptziel der vorliegenden Arbeit war es, ein Schwerlast-EHA-System mit mehrfachen Betätigungseinheiten durch Einführung von umfassenden Perspektiven zu optimieren. Durch Einführung der sog. ganzheitlichen Leichtbauweise demonstriert die Arbeit, wie das Subsystem mit mehreren Endgeräten ultimativ optimiert werden kann, ohne Abstriche an Gewichtsbilanz u/o Kompromiß mit der Energieeffizienz zu machen. Um eine wahrhaftige Optimierung, d.h. die Erreichung des ultimativen, Nonplusultra-Verbesserungslevels zu erreichen, wurden die Systemarchitektur, die Hardware und die Operationsmethode interaktiv kombiniert, wobei die besondere Aufmerksamkeit auf die interaktiven, zur Verbesserung führenden Einflüsse gelegt wurde. Die Minimierung des Energieverbrauchs und die ultimative Gewichtsoptimierung gleichzeitig können erreicht werden, wenn die physikalischen Zusammenhänge zwischen den involvierten Subsystemen verstanden und ihre verborgenen Potentiale ausgenutzt werden. Der einzige und vernünftige Weg zur Erreichung der ultimativen Optimierung eines Betätigungssystems ist eine allumfassende Betrachtung, also eine ganzheitliche Betrachtungs- bzw. Vorgehensweise.
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Rybo, Frida, and Alfred Söder. "Next generation expedition stove : A lead user approach to product development." Thesis, KTH, Maskinkonstruktion (Avd.), 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-277902.
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In 1996 Primus launched their expedition stove Multifuel, the first stove that could run on liquified petroleum gas (LPG), white gas, kerosene and aviation fuel. The multi-fuel stoves are part of the Primus expedition range of equipment. The line was designed and built to perform in extreme conditions. The expedition stoves have been roughly the same since then. Therefore Primus wanted to investigate what the future looks like for these stoves. The expedition segment is very important to the company as it reflects their heritage. Primus had an internal goal of updating the expedition line within the next few years, which was the main reason why this master thesis project arose. The purpose of the project was to investigate the usability of expedition line stoves and understand the user needs to find a direction for the next generation of expedition stoves. The goal was to deliver product development guidelines that Primus can make use of in the continued work as well a well-motivated concept and recommendations for future development based on these guidelines. The work has been carried out applying an adapted lead user approach, meaning some chosen users have been involved throughout the whole development process. Extensive research was made including interviews and user studies. The qualitative data was analysed with inspiration from the Gioia framework and resulted in product development guidelines including insights from the analysis, a user-centered re-segmentation of Primus’ expedition stove line and identification of whitespace. It became evident that an expedition gas stove should be included in the segment as professional users show great will to use gas and the need for multi-fuel is low. Based on the guidelines and user involvement a validated product concept was brought forth. The Primus Altitude Ti is an expedition gas stove in titanium with a flame spreading laminar flow burner providing silent and fuel efficient cooking. The stove has a regulated valve at the burner and an ON/OFF valve at the canister allowing to run the stove in liquid feed mode which is beneficial in cold conditions.År 1996 lanserade Primus sitt expeditionskök Multifuel, vilket var det första köket som kunde användas med gasol, kemiskt ren bensin, fotogen och flygbränsle. Multifuel och ytterligare två flerbränslekök är idag en del av företagets expeditionssegment, som designades för att prestera under extrema förhållanden. Expeditionsköken har inte förändrats avsevärt sedan de togs fram, vilket ledde till att Primus ville undersöka hur framtiden för dessa kök ser ut. Eftersom expeditionsköken symboliserar företagets arv är det ett viktigt segment för dem. Primus satte upp ett internt mål att uppdatera expeditionssegmentet inom de närmsta åren, vilket var huvudorsaken till att detta examensarbete utfördes. Syftet med projektet var att undersöka användarvänligheten hos expeditionsköken och förstå användarnas behov för att på så sätt besluta om en riktning för nästa generations expeditionskök. Målet med arbetet var att leverera både riktlinjer för kommande produktutveckling och ett välmotiverat produktkoncept som är baserat på de framtagna riktlinjerna. Under arbetets gång har en anpassad variant av lead user-metoden använts, vilket betyder att ett antal utvalda användare med värdefulla egenskaper har involverats genom arbetsprocessen. Omfattande undersökningar har gjorts genom bland annat intervjuer och användarstudier. Den kvalitativa datan analyserades med inspiration av Gioia-metodologin och resulterade i en överlämning med riktlinjer för produktutveckling. Detta innefattar insikter från analysen, en användarcentrerad omsegmentering av Primus expeditionssegment samt en identifiering av luckor på marknaden. Det blev tydligt att ett expeditionsgaskök borde inkluderas i segmentet eftersom professionella användare visade stor vilja att använda gas och behovet för flerbränslekök var litet. Baserat på riktlinjerna togs ett produktkoncept fram. Primus Altitude Ti är ett expeditionsgaskök mestadels bestående av titan med en bred brännare som använder sig av tekniken för ett laminärt flöde, vilket ger en tyst och bränsleeffektiv användning. Köket har en steglös ventil vid brännaren samt en ventil med två lägen, på och av, vid gasbehållaren som tillåter drift av köket med gasbehållaren uppochned vilket är fördelaktigt vid kalla förhållanden.
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Hibbert, Kirk R. "A need for systems architecture approach for next generation mine warfare capability." Thesis, Monterey, Calif. : Springfield, Va. : Naval Postgraduate School ; Available from National Technical Information Service, 2006. http://library.nps.navy.mil/uhtbin/hyperion/06Sep%5FHibbert.pdf.
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Thesis (M.S. in Systems Engineering)--Naval Postgraduate School, September 2006.Thesis Advisor(s): John Osmundson, Martha Jallim Hall. "September 2006." Includes bibliographical references (p. 79-83). Also available in print.
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Heslop, Janelle Nicole. "A systematic approach for assessing next generation technologies and solutions in biomanufacturing." Thesis, Massachusetts Institute of Technology, 2019. https://hdl.handle.net/1721.1/122586.
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Thesis: M.B.A., Massachusetts Institute of Technology, Sloan School of Management, 2019, In conjunction with the Leaders for Global Operations Program at MITThesis: S.M., Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, 2019, In conjunction with the Leaders for Global Operations Program at MIT
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 92-93).
Amgen is one of the world's leading independent biotechnology companies and competes globally to advance important medicines in a highly competitive marketplace. Biologics manufacturers such as Amgen have traditionally invested in costly, large-scale stainless steel infrastructure to support the production of biologic medication. However, more recently, changes in the economics, such as the need to deploy less-capital intensive biomanufacturing plants faster, and advances in the technology, such as process-intensification (i.e., getting more protein from each cell), have created both incentives and pressures for smaller-scale, single-use, and modular production technologies. These incentives include greater flexibility, shorter timelines for construction / rapid deployment of new facilities, and reduced costs as well as physical and environmental footprint.
To prepare for this changing business environment, Amgen must develop a manufacturing strategy that can enable the production of high quality products with significant reduction in timelines, cost, and reduced impact. To do so, Amgen is investigating a handful of these new production technologies, known as next generation manufacturing technologies, and attempting to understand their applicability in their future manufacturing model. There is a need for a transparent and standard methodology for evaluating and deploying new technologies in the manufacturing network. This study aims to address this issue and enable speed, rigor, and efficiency of decisionmaking through the use of a structured framework for selection and deployment of next generation technologies. Through literature review and engagement with Amgen experts, this study defines a next generation manufacturing technology evaluation framework.
This framework involves a hybrid, multi-attribute set of metrics that are broadly categorized into economic, environmental, and operational assessment areas. The framework is then applied to assess the economic, operational, and environmental implications of deploying single use technologies in drug substance manufacturing as a test of concept. An assessment along the three areas helps to identify that single use technologies, namely single use bags due to their cost and environmental footprint, may not always be the optimum substitute for all existing process technology. Instead, a hybrid approach, mixing new single use technology with existing stainless steel infrastructure, may help to reduce variable cost and carbon footprint of the process.
When the framework and this proposed hybrid approach was at an Amgen site, a potential savings of up to $ 1 M per year was identified as well as the elimination of up to thousands of liters in clean water losses, and up to 400x reduction in the carbon footprint of the process. Lastly, the assessment framework is applied as a management tool in the assessment of next generation drug product filling technology to demonstrate how the framework can be used to enable rapid decision-making related to future manufacturing scenarios.
by Janelle Nicole Heslop.
M.B.A.
S.M.
M.B.A. Massachusetts Institute of Technology, Sloan School of Management
S.M. Massachusetts Institute of Technology, Department of Civil and Environmental Engineering
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Okwo, Adaora. "Next-generation biofuels: the supply chain approach to estimating potential land-use change." Diss., Georgia Institute of Technology, 2012. http://hdl.handle.net/1853/47603.
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Biofuels, including ethanol and biodiesel, are important components of energy policy in the U.S. and abroad. There is a long history of ethanol production from corn (maize) in the United States and from sugarcane in Brazil. However, there has been a push for greater use of next-generation biofuels (including those derived from cellulosic feedstocks) to mitigate many of the environmental and potential food system impacts of large scale biofuel production.
Farmer willingness to grow biomass crops and ensuring adequate feedstock supply are two important challenges impeding large scale commercialization of next-generation biofuels. The costs of transporting bulky, low density biomass will be substantial. Consequently, in the near term, the economic success of next-generation biofuels will hinge on the supply of locally available biomass. As such, agricultural contracts are expected to be an important tool in overcoming the feedstock acquisition challenge. The broad objective of this study is to understand the effect of contracting for non-food energy crops (cellulosic feedstocks) on the agricultural landscape via the displacement of commodity (food) crops on productive cropland.
We develop an analytical framework for evaluating the design and use of two different contract structures for securing cellulosic feedstock in a representative supply chain with a biorefinery and farmer. We study the dynamics of scarce land and indirect competition from commodity market production on a biorefinery's equilibrium pricing strategy and the resultant supply of cellulosic biomass. And we consider its sensitivity to various production characteristics and market conditions.
We develop a method for quantifying the biorefinery's tradeoff between profit margins and competing for land in order to secure the requisite feedstock for biofuel production. And we characterize the loss of efficiency in the decentralized system, relative to a vertically integrated system, that can be attributed to the need to compete for the farmer's scarce land resource versus that which results from the biorefinery's desire to make a profit.
Then we extend our framework to consider multi-year contracts for biomass production and evaluate the importance of land quality, yield variability and contract structure on a farmer's willingness to accept a contract to produce cellulosic feedstock as well as the resulting impact on the agricultural landscape through the displacement of commodity crops. Using switchgrass production in Tennessee as a case study, we develop feedstock supply curves for each contract structure considered and evaluate the conditions and contract prices at which land devoted to various field crops would be displaced by switchgrass based on field trials of switchgrass production in Tennessee and recent USDA data on crop prices and production.
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Nguyen, Thien. "Coordinated behavior for predator prey modeling an approach to next generation console development /." [Gainesville, Fla.] : University of Florida, 2008. http://purl.fcla.edu/fcla/etd/UFE0022893.
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Sung, Che-ming, and 宋志明. "A network approach to the study of the next generation in the mobile telephone market." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1995. http://hub.hku.hk/bib/B31266824.
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Sung, Che-ming. "A network approach to the study of the next generation in the mobile telephone market /." Hong Kong : University of Hong Kong, 1995. http://sunzi.lib.hku.hk/hkuto/record.jsp?B1470898X.
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Silva, Hector E. "Enterprise design for services : a systems approach for the Boeing next generation corporate travel system architecture." Thesis, Massachusetts Institute of Technology, 2010. http://hdl.handle.net/1721.1/59171.
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Thesis (M.B.A.)--Massachusetts Institute of Technology, Sloan School of Management; and, (S.M.)--Massachusetts Institute of Technology, Engineering Systems Division; in conjunction with the Leaders for Global Operations Program at MIT, 2010.Cataloged from PDF version of thesis.
Includes bibliographical references (p. 72).
Typically a company's second largest controllable expense, corporate travel affects many employees at Boeing. A challenge when implementing improvements in the travel and expense system, which is actually comprised of a system of systems, is the coordination of various solutions to ensure improvements in one area do not adversely affect the efficiency of other areas. Various systems along with the people, policies, and processes used to provide services to travelers must be coordinated both inside and outside Boeing in order for overall travel operations to function properly. The intent of this project is to establish a systems-based architecture for Boeing's Next Generation Travel System. This thesis proposes re-designing the Boeing travel system using an enterprise architecting framework to select a future state architecture for a service organization. The analysis recommends a supplier integrated "off-the-shelf' software solution, employing the software as a service business model. Under this model the supplier is paid per transaction completed in the system; adoption of this metric aligns the system to reduce re-work costs, increase first-time pass quality, and improve usability. Additionally, new supplier software tools will allow the Boeing travel organization to transition from a process-focused to a more knowledge-focused service team.
by Hector E. Silva.
S.M.
M.B.A.
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Moreno, Cabrera José Marcos. "A translational bioinformatics approach to improve genetic diagnostics of hereditary cancer using next-generation sequencing data." Doctoral thesis, Universitat de Barcelona, 2021. http://hdl.handle.net/10803/672364.
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This PhD thesis has been carried out with the aim of improving, from a bioinformatic-based approach, the genetic diagnostics of hereditary cancer. More specifically, the aims were:
1. To perform a comprehensive evaluation of tools suitable for detecting CNVs from NGS panel data at single-exon resolution.
2. To select the best candidate tool to implement in the genetic diagnostics pipeline of the ICO-IGTP program on hereditary cancer.
3. After implementing it, to evaluate the impact of including the selected NGS CNV detection tool as a first-tier screening step prior to MLPA validation.
4. To develop a tool to identify false positives produced by germline NGS CNV detection tools.
5. To develop a web-based tool to support the entire diagnostic process during the laboratory routine.
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Yu, Zehao. "Towards location-awareness in next generation wireless networks : a new approach based on channel state information." Thesis, Massachusetts Institute of Technology, 2020. https://hdl.handle.net/1721.1/127117.
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Thesis: S.M., Massachusetts Institute of Technology, Department of Aeronautics and Astronautics, May, 2020Cataloged from the official PDF of thesis.
Includes bibliographical references (pages 69-78).
Location-awareness in next generation wireless networks will be a key enabler for numerous emerging applications. Recently, a novel approach to localization based on soft information (SI), exploiting all positional information inherent in measurement and contextual data, has been proposed. This thesis further develops SI-based localization by establishing a new approach relying on channel state information (CSI) measurements. In particular, we design an efficient joint message-passing (MP) localization algorithm, which consists of two layers: the transformation layer and the estimation layer. The transformation layer extracts SI of the channel impulse response (CIR) from CSI measurements using a sparsity promoting prior model, which addresses the difficulty of unknown number of multipath in estimating the CIR. The estimation layer infers node positions based on the SI of the CIR using a delay-origin uncertainty model, which describes the conditional distribution of the delays in the CIR given node positions. Simulation results using QuaDriGa channel simulator show that our localization algorithm achieves decimeter-level localization accuracy for both Wi-Fi and mmWave signals, which outperforms conventional algorithms.
by Zehao Yu.
S.M.
S.M. Massachusetts Institute of Technology, Department of Aeronautics and Astronautics
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Ying, Daidong. "Energy-Efficient and Secure Device-to-Device Communications in the Next-Generation Wireless Network." University of Dayton / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=dayton1532458376184496.
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Candelli, Tito. "NOVEL APPROACH TO STORAGE AND STORTING OF NEXT GENERATION SEQUENCING DATA FOR THE PURPOSE OF FUNCTIONAL ANNOTATION TRANSFER." Thesis, Högskolan i Skövde, Institutionen för vård och natur, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-6043.
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The problem of functional annotation of novel sequences has been a sigfinicant issue for many laboratories that decided to apply next generation sequencing techniques to less studied species. In particular experiments such as transcriptome analysis heavily suer from this problem due to the impossibility of ascribing their results in a relevant biological context. Several tools have been proposed to solve this problem through homology annotation transfer. The principle behind this strategy is that homologous genes share common functions in dierent organisms, and therefore annotations are transferable between these genes. Commonly, BLAST reports are used to identify a suitable homologousgene in a well annotated species and the annotation is then transferred fromthe homologue to the novel sequence. Not all homologues, however, possess valid functional annotations. The aim of this project was to devise an algorithm to process BLAST reports and provide a criterion to discriminate between homologues with a biologically informative and uninformative annotation, respectively. In addition, all data obtained from the BLAST report isto be stored in a relational database for ease of consultation and visualization. In order to test the solidity of the system, we utilized 750 novel sequences obtained through application of next generation sequencing techniques to Avena sativa samples. This species particularly suits our needs as it represents the typical target for homology annotation transfer: lack of a reference genome and diculty in attributing functional annotation. The system was able to perform all the required tasks. Comparisons between best hits asdetermined by BLAST and best hits as determined by the algorithm showed a significant increase in the biological significance of the results when thealgorithm sorting system was applied.
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Kwok, Wing Hei Harold. "New Approach in Fabrication of Solid-State Nanopore for Bio-Sensing Applications." Thesis, Université d'Ottawa / University of Ottawa, 2015. http://hdl.handle.net/10393/32210.
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The 21st century marks the defining point of human history in terms of technological advancement. In 2014, we were at the edge of acquiring a complete understanding of the fundamental construct to all life forms. The capability to manipulate and recreate lives as desired will soon be at our hands and will eventually lead to the redefinition of life and humanity. This brave new world, for better or worse, will be stitched together by scientific breakthroughs in many disciplines.
Nanopore fluidic system – and microfluidic in general – might be one of the key puzzles towards the future. It is seen as a likely candidate for the next generation of rapid and low-cost genetic sequencing technology, which will allow us to gain thorough insight into the genetic code of every living organism on earth. It can also have the capability to individually detect and manipulate virtually any biological molecules, possibly allowing it to be a universal diagnostic tool or a bio-molecule synthesiser. The future of nanopore fluidic system is prosperous, but the difficulties are equally challenging. Currently, both biological and solid-state nanopores are non-trivial to create. For instance, a small solid-state nanopore can only be fabricated with expansive machinery in a low-yield, low-throughput manner.
To overcome this challenge, a new set of methods involving high electric field to fabricate and enlarge a solid-state nanopore has been developed. It was found that a nanopore, when subjected to a high electric field, can be enlarged in angstrom increments and cleared of unidentified obstructions that cause low-frequency ionic current fluctuations. It was also found that an intact solid-state membrane, when subjected to a high electric field for a period of time, can leave a single nanopore imprinted onto it. The process of creation is best describe as a dielectric breakdown event and can be modeled by the percolation theory for dielectric breakdown. The resulting nanopores are cylindrical in shape and are shown to be equally capable of single molecule sensing compare to pores created by other methods. To accommodate future nanopore designs and applications and to examine the scope of applicability of the new fabrication approach, more advanced nanopore devices were created on some dual-layer solid-state membranes comprising of a metallic and a dielectric layer. Experiments indicated that the method could indeed create nanopore on such advanced membranes. It was further shown that the metallic layer receded further than the dielectric layer, forming a hollow conical shape at the opening of the dielectric nanopore. Such metalized bi-layer nanopore system was found to interact strongly with short single stranded DNA molecules, resulting in prolonged DNA translocation time. A simple picture of the mechanism was proposed to explain the observation. Lastly, to extend the limit of the new fabrication approach, I attempted to fabricate nanopore on complex multi-layer membranes involving a graphene film sandwiched in several dielectric materials. It was found that the quality of the graphene film and the transfer method were vital to the success of this project. Nevertheless, preliminary results indicated that the new method could create a nanopore through this complex multi-layer membrane.
The new method to fabricate and tune both simple and complex nanopores is amongst the simplest, the least costly and the most efficient one that one can imagine. The research work has already sparked a dramatic increase in scientific throughput in our laboratory and other laboratories we had collaboration with. It fueled more than a dozen projects and involved close to a thousand nanopores in total. Such projects are far from possible if they were to rely on conventional fabrication methods. However, these are insignificant if we consider the new method is simple enough that, for the very first time, general public can easily access nanofabrication and single-molecule manipulation technology. The liberation of nanotechnology to the general public symbolically marks the beginning of a brave new world.
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Alvarez, Rodriguez Alberto. "An integrated framework for the next generation of Risk-Informed Performance-Based Design approach used in Fire Safety Engineering." Digital WPI, 2013. https://digitalcommons.wpi.edu/etd-dissertations/5.
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Review of decades of worldwide experience using standards, codes and guidelines related to performance-based fire protection design for buildings has identified shortcomings in the interpretation, application and implementation of the performance-based design process, wide variation in the resulting levels of performance achieved by such designs, and several opportunities to enhance the process. While others have highlighted shortcomings in the past, as well as some ideas to enhance the process, it is proposed that a more fundamental change is needed. First, the political and technical components of the process need to be clearly delineated to facilitate better analysis and decision-making within each component. Second, the process needs to be changed from one which focuses only on fire safety systems to one which views buildings, their occupants and their contents as integrated systems. In doing so, the activities associated with the normal operation of a building and how they might be impacted by the occurrence of a fire event become clearer, as do mitigation options which account for the behaviors and activities associated with normal use. To support these changes, a new framework for a risk-informed performance-based process for fire protection design is proposed: one which is better integrated than current processes, that treats a fire event as a disruptive event of a larger and more complex "building-occupant" system, and that provides more specific guidance for engineering analysis with the aim to achieve more complete and consistent analysis. This Ph.D. Dissertation outlines the challenges with the existing approaches, presents the "building-occupant" system paradigm, illustrates how viewing fire (or any other hazard) as a disruptive event within an holistic "building-occupant" system can benefit the overall performance of this system over its lifespan, and outlines a framework for a risk-informed performance-based process for fire protection design. Case studies are used to illustrate shortcomings in the existing processes and how the proposed process will address these. This Dissertation also includes a plan of action needed to establish guidelines to conduct each of the technical steps of the process and briefly introduces the future work about how this plan could be practically facilitated via a web-platform as a collaborative environment.
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Somavarapu, Sashi K. (Sashi Kanth). "System dynamics approach to understand the role of information technology in the evolution of next generation integrated product development systems." Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/33419.
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Thesis (S.M.)--Massachusetts Institute of Technology, System Design and Management Program, 2005.Includes bibliographical references (p. 96-97).
For the automotive industry, to be competitive in the market place has to devise many strategies. Some of the prominent strategies include and are not limited to, reduction of development costs by moving in-house work to its suppliers, reduction of PD cycle time by mimicking some of the industry's successful PD processes. Some companies are also devising some complex strategies like Zero-Prototype development using computer aided prototyping and testing, currently prevalent in the aerospace and naval industries, and more recently making a move into the Lean PD systems and processes to avoid waste and increase efficiency. However, to introduce such lean PD systems, with reduced PD cycle time, into a complex organization with many internally developed IT systems, processes and tools is a huge challenge. The organization needs to adapt to these lean environments not just structurally but also culturally. To design a lean PD organization (system) the decision makers have to foresee and understand how the system of systems may react to the change before they are implemented and/or executed. In the past couple of decades IT systems have been a primary enabler for PD work flow processes.
(cont.) However, IT systems are so engraved in some PD organizations that they have turned into an engineering process mechanism. Also, some of the IT systems have served more than their life expectancy and in some cases cannot be decommissioned because these systems are so tightly coupled with the business processes. An understanding of the internal system dynamics of these deeply engraved IT systems in the PD life cycle will help the automotive industry executives (decision makers) and IT systems architects to make the right decision when designing and deploying the new PD systems or processes. This study provides an overview of how IT tools have evolved in the automotive industry. Extensive research was conducted to understand the different system dynamics tools used in industry - specifically in automotive product development and the software development areas. The study concludes with an explanation of how system dynamics tools can be used as a program planning and management tool.
by Sashi K. Somavarapu.
S.M.
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Coetzee, Beatrix. "A metagenomic approach using next-generation sequencing for viral profiling of a vineyard and genetic characterization of grapevine virus E." Thesis, Stellenbosch : University of Stellenbosch, 2010. http://hdl.handle.net/10019.1/5186.
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Thesis (MSc (Genetics))--University of Stellenbosch, 2010.Includes bibliography.
Title page: Dept. of Genetics, Faculty of Science
ENGLISH ABSTRACT: Next-generation sequencing technologies are increasingly used in metagenomic studies, largely due to the high sequence data throughput capacity and unbiased approach in determining the genetic composition of an unknown environmental sample. This study investigated the applicability of the Illumina next-generation sequencing platform for metagenomic sequencing of grapevine viruses to provide the first complete viral profile, or virome, of a diseased vineyard. Leaf material was harvested from 44 randomly selected vines in a leafroll-diseased vineyard in South Africa. Sample material was pooled and double-stranded RNA extracted. The dsRNA was sequenced as a paired-end sequencing run using the Illumina sequencing-by-synthesis technique, and more than 19 million sequence reads, equivalent to approximately 837 megabases of metagenomic sequence data, were obtained. Of these data, approximately 400 megabases could be assembled into 449 scaffolds, using the de novo assembler Velvet. These scaffolds were subjected to BLAST searches against the NCBI databases and top hit scores were used for virus identification. Based on the BLAST results, suitable sequences were selected from the NCBI database and used as reference sequence in MAQ mapping assemblies. The bioinformatic analyses allowed for the determination of the virus species present, the most prominent variants, and the relative abundance of each. Four known grapevine viral pathogens were identified. Grapevine leafroll-associated virus 3, representing 59% of the analyzed short read sequence data, was identified as the most prominent virus species. Three variants of this virus were detected: GP18 was the most abundant, followed by a minor Cl766/NY1 variant and a potential novel grapevine leafroll-associated ampelovirus. A single Grapevine rupestris stem pitting ]associated virus variant, similar to SG1, and a Grapevine virus A variant, a member of molecular group III, were identified. This study is also the first to report the presence of Grapevine virus E (GVE) in South African vineyards. Grapevine virus E was further genetically characterized and the genome sequence of GVE isolate SA94 determined. The GVE SA94 genome sequence, 7568 nucleotides in length, is the first complete genome sequence for the virus species. The genome organization of GVE SA94 is typical of vitiviruses, but in contrast to other RNA viruses, the AlkB domain is located within the helicase domain in open reading frame 1 (ORF 1). Grapevine virus E SA94 shares nearly 100% nucleotide identity with the Japanese TvP15 isolate and GVE 3404, a de novo scaffold generated from the metagenomic sequence data. Bioinformatic analysis of metagenomic sequence data further revealed the presence of three fungus-infecting viral families, Chrysoviridae, Totiviridae and the unclassified dsRNA virus, Fusarium graminearum dsRNA mycovirus 4. A virus from the family Chrysoviridae, similar to Penicillium chrysogenum virus, was the second most abundant virus detected. We demonstrated the successful application of a short read sequencing technology, such as the Illumina platform, for viral profiling of an infected vineyard. To our knowledge this is the first application of the Illumina technology for this purpose.
AFRIKAANSE OPSOMMING: Volgende-generasie tegnologie om basis volgordes van nukleiensure te bepaal, word al meer gebruik in metagenomiese studies. Dit is veral weens die hoe data-omset kapasiteit en onbevooroordeelde aanslag in die bepaling van die genetiese samestelling van onbekende omgewingsmonsters. Hierdie studie het die aanwending van die Illumina volgende-generasie volgorde-bepalingsplatform in 'n metagenomiese studie van wingerdvirusse, ondersoek. Dit het ten doel gehad om die eerste volledige virus profiel, of viroom, van 'n geinfekteerde wingerd saam te stel. Blaarmateriaal is verkry vanaf 44 lukraak-gekose wingerdstokke in 'n rolblad-geinfekteerde wingerd in Suid-Afrika. Monster materiaal is saamgevoeg en dubbelstring-RNS geekstraheer. Die dubbelstring-RNS is onderwerp aan gepaarde-ent volgorde-bepaling deur gebruik te maak van die Illumina volgorde-bepaling-deur-sintese tegniek. Meer as 19 miljoen volgorde reekse, ekwivalent aan ongeveer 837 megabasisse volgorde data, is verkry. Van hierdie data kon ongeveer 400 megabasisse saamgevoeg word in 449 konstrukte ("scaffolds"), deur gebruik te maak van die de novo samesteller Velvet. Hierdie konstrukte is onderwerp aan BLAST soektogte teen die NCBI databasisse en die hoogste trefslag-telling is gebruik vir virus identifikasie. Op grond van die "BLAST" resultate is geskikte volgordes geselekteer vanaf die NCBI databasis en gebruik as verwysingvolgordes in MAQ kartering-analises. Met die bioinfomatika analises kon die virus spesies teenwoordig, asook die mees prominente variante en relatiewe voorkoms van elk, bepaal word. Vier bekende virus wingerdpatogene is geidentifiseer. Grapevine leafroll-associated virus 3, verteenwoordig deur 59% van die geanaliseerde kort-reeks volgorde data, is identifiseer as die mees prominente virus spesie. Drie variante van die virus is in die wingerdmonster opgespoor: GP18 kom die mees algemeen voor, gevolg deur 'n CL-766/NY1 variant en 'n potensiele nuwe wingerd rolblad-geassosieerde ampelovirus. 'n Enkele Grapevine rupestris stem pitting-associated virus variant, soortgelyk aan SG1, en 'n Grapevine virus A variant, 'n lid van molekulere groep III, is geidentifiseer. Hierdie studie is ook die eerste om die teenwoordigheid van Grapevine virus E (GVE) in Suid-Afrikaanse wingerde te rapporteer. Grapevine virus E is verder geneties gekarakteriseer en die genoomvolgorde van GVE isolaat SA94 is bepaal. Die GVE SA94 genoomvolgorde, 7568 nukleotiede lank, is die eerste volledige genoomvolgorde vir hierdie virus spesie. Die genoomorganisasie is tipies van vitivirusse, maar in kontras met ander RNA virusse is die AlkB domein binne-in die helikase domein van oopleesraam 1 (ORF 1) geleë. Grapevine virus E SA94 deel byna 100% nukleotied identiteit met die Japannese TvP15 isolaat en GVE 3404, 'n de novo konstruk gegenereer vanaf die metagenomiese volgorde data. Bioinformatika analises van die metagenomiese volgorde data het verder die teenwoordigheid van drie swam-infekterende virus families, die Chrysoviridae, Totiviridae en ongeklassifiseerde dubbelstring-RNS virus, Fusarium graminearum dsRNA mycovirus 4, aangetoon. 'n Virus van die Chrysoviridae familie, soortgelyk aan Penicillium chrysogenum virus, het die tweede meeste voorgekom in die wingerd monster. Hierdie studie demonstreer die suksesvolle toepassing van 'n kort reeks volgorde-bepalingstegnologie soos die Illumina platform, vir die opstel van 'n virusprofiel van 'n geinfekteerde wingerd. Sover ons kennis strek is hierdie die eerste aanwending van die Illumina tegnologie vir hierdie doel.
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Labuschagne, Jan Phillipus Lourens. "Development of a data processing toolkit for the analysis of next-generation sequencing data generated using the primer ID approach." University of the Western Cape, 2018. http://hdl.handle.net/11394/6736.
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Philosophiae Doctor - PhDSequencing an HIV quasispecies with next generation sequencing technologies yields a dataset with significant amplification bias and errors resulting from both the PCR and sequencing steps. Both the amplification bias and sequencing error can be reduced by labelling each cDNA (generated during the reverse transcription of the viral RNA to DNA prior to PCR) with a random sequence tag called a Primer ID (PID). Processing PID data requires additional computational steps, presenting a barrier to the uptake of this method. MotifBinner is an R package designed to handle PID data with a focus on resolving potential problems in the dataset. MotifBinner groups sequences into bins by their PID tags, identifies and removes false unique bins, produced from sequencing errors in the PID tags, as well as removing outlier sequences from within a bin. MotifBinner produces a consensus sequence for each bin, as well as a detailed report for the dataset, detailing the number of sequences per bin, the number of outlying sequences per bin, rates of chimerism, the number of degenerate letters in the final consensus sequences and the most divergent consensus sequences (potential contaminants). We characterized the ability of the PID approach to reduce the effect of sequencing error, to detect minority variants in viral quasispecies and to reduce the rates of PCR induced recombination. We produced reference samples with known variants at known frequencies to study the effectiveness of increasing PCR elongation time, decreasing the number of PCR cycles, and sample partitioning, by means of dPCR (droplet PCR), on PCR induced recombination. After sequencing these artificial samples with the PID approach, each consensus sequence was compared to the known variants. There are complex relationships between the sample preparation protocol and the characteristics of the resulting dataset. We produce a set of recommendations that can be used to inform sample preparation that is the most useful the particular study. The AMP trial infuses HIV-negative patients with the VRC01 antibody and monitors for HIV infections. Accurately timing the infection event and reconstructing the founder viruses of these infections are critical for relating infection risk to antibody titer and homology between the founder virus and antibody binding sites. Dr. Paul Edlefsen at the Fred Hutch Cancer Research Institute developed a pipeline that performs infection timing and founder reconstruction. Here, we document a portion of the pipeline, produce detailed tests for that portion of the pipeline and investigate the robustness of some of the tools used in the pipeline to violations of their assumptions.
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Mori, Minako. "Pathogenic mutations identified by a multimodality approach in 117 Japanese Fanconi anemia patients." Kyoto University, 2019. http://hdl.handle.net/2433/243302.
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Seung, Taehun [Verfasser], Lothar [Akademischer Betreuer] Kroll, Lothar [Gutachter] Kroll, and Piotr [Gutachter] Gendarz. "Holistic-Lightweight Approach for actuation systems of the next generation aircraft / Taehun Seung ; Gutachter: Lothar Kroll, Piotr Gendarz ; Betreuer: Lothar Kroll." Chemnitz : Universitätsverlag Chemnitz, 2019. http://d-nb.info/1219581917/34.
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Basu, Piyali. "A novel whole system integrated genomics approach to identify key genetic components which facilitate synthetic design of a genetically engineered strain of Escherichia coli K12 with enhanced isobutanol tolerance." Thesis, Brunel University, 2016. http://bura.brunel.ac.uk/handle/2438/13712.
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There has been an increased global interest in biofuels which provide a renewable and sustainable alternative to fossil fuels. Isobutanol is an attractive and superior alternative to the currently produced bioethanol possessing several key advantages. Previous work focuses on strategies for metabolic optimisation of carbon utilisation. However, existing solutions reach a stage where the amount of alcohol produced reaches toxic thresholds for bacteria. This inhibits growth and reduces carbohydrate consumption resulting in lower product yields rendering the biofuel production process uneconomical. In this project, a novel strategy has been adopted which uses a whole system integrated genomics approach consisting of expression profiling, selection to create isobutanol-adapted lineages, next generation sequencing, and comparative behavioural genomics to interrogate the system thoroughly and identify critical determinants of resistance to isobutanol. These were used in the highly-defined model species, E. coli K12 to deliver results of the adaptive mechanisms which take place across the entire genome. 41 gene candidates (4 previously identified in literature) were identified to play a role in isobutanol tolerance. These candidates belong to a range of functional groups such as carbohydrate metabolism, oxidative stress response, osmotic stress response; but also identified novel membrane-associated functions such as the Tol-Pal system, BAM complex and colanic acid production. The results also identify critical genes with unknown functions. The results support previous notions that central carbon metabolism shifts from aerobic to anaerobic metabolism in the presence of isobutanol, but also shows there is a transitionary phase where mixed acid fermentation pathways are utilised. This shift was previously thought to be mediated by the ArcA-ArcB two-component system. However, these results suggest the inactive 2Fe-2S core of the anaerobic-regulator Fnr is re-activated by Fe2+ to form the 4Fe-4S core transported by the FeoAB ferrous iron transport system. The strategy also identified the Tol-Pal system and show it is essential to grow in the presence of isobutanol, which is responsible for the maintaining the integrity of the cell envelope structure and increasing the rate of cell division. The BAM complex is responsible for folding and assembly of outer membrane proteins (OMP) and OMP membrane permeability- this system was found to be important for growth in isobutanol, and SurA, which is the primary OMP assembly pathway provided tolerance which was specific to isobutanol. Colanic acid, an extracellular polysaccharide is produced when the cell experiences stress, and provides protection by forming a physical barrier around the cell. The results show that the presence of colanic acid plays a large role in allowing E. coli to grow in presence of isobutanol, and its role becomes essential at critical concentrations. The results also show deletion of the negative regulator of the colanic acid gene cluster improves growth at critical and growth-inhibiting concentrations. When consolidated, these results facilitated knowledge-led based design and subsequently led to the identification of components for a synthetic design schedule, which lists the genetic manipulations proposed to exploit E. coli to enhance isobutanol tolerance.
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Nguyen, Viet Tuan. "An evaluation of potential candidate genes involved in salinity tolerance in striped catfish (Pangasianodon hypopthalmus) using an RNA-SEQ approach." Thesis, Queensland University of Technology, 2015. https://eprints.qut.edu.au/84924/4/Viet_Tuan_Nguyen_Thesis.pdf.
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The project investigated the molecular response of Tra catfish (Pangasianodon hypophthalmus) to elevated salinity conditions. We employed Next generation sequencing platform to evaluate differential gene expression profiles of key genes under two salinity conditions. Results of the current project can form the basis for further studies to confirm the functional roles of specific genes that influence salinity tolerance in the target species and more broadly in other freshwater teleost fishes. Ultimately, the approach can contribute to developing superior culture stocks of the target species.
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Robertson, Laura, Andrea Lowery, Lindsay Lester, and Renee Rice Moran. "The Intersection of 5Es Instruction, and the Claims, Evidence, and Reasoning Framework: A Hands-on Approach Supporting the NGSS in Upper Elementary Classrooms." Digital Commons @ East Tennessee State University, 2018. https://dc.etsu.edu/etsu-works/1308.
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Pinney, Brian Robert John. "Characterizing the changes in teaching practice during first semester implementation of an argument-based inquiry approach in a middle school science classroom." Diss., University of Iowa, 2013. https://ir.uiowa.edu/etd/4721.
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The purpose of this study was to characterize ways in which teaching practice in classroom undergoing first semester implementation of an argument-based inquiry approach changes in whole-class discussion. Being that argument is explicitly called for in the Next Generation Science Standards and is currently a rare practice in teaching, many teachers will have to transform their teaching practice for inclusion of this feature. Most studies on Argument-Based Inquiry (ABI) agree that development of argument does not come easily and is only acquired through practice.
Few studies have examined the ways in which teaching practice changes in relation to the big idea or disciplinary core idea (NGSS), the development of dialogue, and/or the development of argument during first semester implementation of an argument-based inquiry approach. To explore these areas, this study posed three primary research questions: (1) How does a teacher in his first semester of Science Writing Heuristic professional development make use of the "big idea"?, (1a) Is the indicated big idea consistent with NGSS core concepts?, (2) How did the dialogue in whole-class discussion change during the first semester of argument-based inquiry professional development?, (3) How did the argument in whole-class discussion change during the first semester of argument-based inquiry professional development?
This semester-long study that took place in a middle school in a rural Midwestern city was grounded in interactive constructivism, and utilized a qualitative design to identify the ways in which the teacher utilized big ideas and how dialogue and argumentative dialogue developed over time. The purposefully selected teacher in this study provided a unique situation where he was in his first semester of professional development using the Science Writing Heuristic Approach to argument-based inquiry with 19 students who had two prior years' experience in ABI. Multiple sources of data were collected, including classroom video with transcripts, teacher interview, researcher field notes, student journals, teacher lesson plans from previous years, and a student questionnaire. Data analysis used a basic qualitative approach.
The results showed (1) only the first time period had a true big idea, while the other two units contained topics, (2) each semester contained a similar use for the given big idea, though its role in the class was reduced after the opening activity, (3) the types of teacher questions shifted toward students explaining their comprehension of ideas and more students were involved in discussing each idea and for more turns of talk than in earlier time periods, (4) understanding science term definitions became more prominent later in the semester, with more stating science terms occurring earlier in the semester, (5) no significant changes were seen to the use of argument or claims and evidence throughout the study.
The findings have informed theory and practice about science argumentation, the practice of whole-class dialogue, and the understanding of practice along four aspects: (1) apparent lack of understanding about big ideas and how to utilize them as the central organizing feature of a unit, (2) independent development of dialogue and argument, (3) apparent lack of understanding about the structure of argument and use of basic terminology with argument and big ideas, (4) challenges of ABI implementation. This study provides insight into the importance of prolonged and persistent professional development with ABI in teaching practice.
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Zegarra, León Zegarra León. "A combinatorial approach to query the PknG interactome of Mycobacterium tuberculosis." Bachelor's thesis, Universidad Peruana de Ciencias Aplicadas (UPC), 2019. http://hdl.handle.net/10757/628099.
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La capacidad de Mycobacterium tuberculosis para sobrevivir dentro del macrófago contribuye grandemente a su patogenicidad, latencia y persistencia durante la infección. Este bacilo induce alteraciones en el ambiente intrafagosomal e inhibe la maduración del fagosoma, favoreciendo su supervivencia intracelular. M. tuberculosis PknG secuestra al macrófago precisamente al evitar la fusión fagosoma-lisosoma. En este sentido, PknG representa una familia de dianas novedosas para enfrentar la necesidad de nuevos antimicrobianos para la tuberculosis latente. Aquí, apuntamos a: (i) elucidar la base estructural-molecular del ATP y Mg2+ como cofactores de PknG; (ii) caracterizar los parámetros cinéticos que gobiernan la formación del complejo PknG:ATP; e, (iii) identificar péptidos capaces de unirse a PknG para investigar experimentalmente su interactoma usando enfoques combinatorios como “Phage Display”. Nuestros resultados confirman que PknG se une exclusivamente al ATP con una constante de disociación (KD) de 108.8 22.9 µM. El Mg2+ estabiliza térmicamente a PknG de forma ATP-dependiente. Análisis de estado pre-estacionario muestran que la unión y disociación del ATP es rápida en el complejo PknG:ATP. Usando PknGN-Ext, TPR resolvimos la estructura cristalina en el estado unido al ADP mientras que demostramos que el ATP imposibilita la cristalización. Los análisis bioinformáticos de las librerías enriquecidas por Phage Display identificaron 57 potenciales peptidos que interactuarían con PknG. Una comparación cercana con el proteoma de M. tuberculosis proporcionó un subconjunto de 20 proteínas que podrían interactuar con PknG. Nuestros resultados confirmaron cinco proteínas asociadas a PknG previamente reportadas: PknG, DnaK chaperona, transportador ABC Rv1747, Proteína Ribosomal L23 y Factor de Elongación Tu, resaltando la validez de nuestra plataforma para descubrir el interactoma de PknG. Así, nuestros resultados revelan interacciones proteína-proteína putativas que podrían participar en la supervivencia micobacteriana, mientras que también proporcionan bases sólidas para desarrollar drogas antituberculosas al interrumpir estas interacciones o explotar estos peptidos tipo compuesto líder.The ability of Mycobacterium tuberculosis to survive inside the macrophage greatly contributes to its pathogenicity, latency and persistence during infection. This bacillus induces alterations in the intraphagosomal environment and inhibits phagosome maturation, thus promoting mycobacterial survival. M. tuberculosis PknG hijacks the macrophage precisely by avoiding phagosome-lysosome fusion. In this sense, PknG represents a family of novel targets to cope with the need for new antimicrobials for latent tuberculosis. Here, we aimed to: (i) elucidate the structural-molecular basis of ATP and Mg2+ as PknG cofactors; (ii) characterize the kinetic parameters governing PknG:ATP complex formation; and, (iii) identify PknG-binding peptides to experimentally query PknG’s interactome using combinatorial approach such as Phage Display. Our results confirm that PknG exclusively binds to ATP with a dissociation constant (KD) of 108.8 22.9 µM. Mg2+ thermally stabilizes PknG in an ATP-dependent manner. Pre-steady-state analyses show that ATP binding and dissociation are rapid in the PknG:ATP complex. Using PknGN-Ext, TPR we solved the ADP-state crystal structure while showing that ATP precludes crystallization. Phage Display and bioinformatic analyses identified 57 potential PknG binders. A close comparison to the M. tuberculosis proteome provided a subset of 20 proteins that may interact with PknG. Our results confirmed five previously reported PknG-associated proteins: PknG, DnaK chaperone, ABC transporter Rv1747, Ribosomal Protein L23 and Elongation Factor Tu, highlighting our platform’s validity to uncover the PknG interactome. Altogether, our results reveal putative protein-protein interactions that may play a role in mycobacterial survival, while also providing solid bases for the development of anti-tuberculosis drugs by disrupting these interactions or exploiting these lead-like peptide molecules.
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Robertson, Laura, Harold Kelley, Scott Honeycutt, and Kari Eubanks. "From Molecules to Organisms (LS1): An Integrated, Hands-on Approach Supporting NGSS and CCSS ELA." Digital Commons @ East Tennessee State University, 2018. https://dc.etsu.edu/etsu-works/1309.
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Robertson, Laura, Renee Rice Moran, Chih-Che Tai, LaShay Jennings, Huili Hong, and Diana O'Neal. "Force and Motion: An Integrated K-8 Hands-On Approach Supporting the NGSS and CCSS ELA." Digital Commons @ East Tennessee State University, 2017. https://dc.etsu.edu/etsu-works/1312.
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Robertson, Laura, LaShay Jennings, Kari Eubanks, and Scott Honeycutt. "Photosynthesis and Cellular Respiration (LS1): A Hands-On Approach Supporting the NGSS and ELA CCSS." Digital Commons @ East Tennessee State University, 2017. https://dc.etsu.edu/etsu-works/1313.
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Kruse, Colin Peter Singer. "Data-Enabled Approach to Characterize Dynamic Regulatory Pathways in Two Kingdoms." Ohio University / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1573746719306039.
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Lacoste, Deixonne Caroline. "Apport du séquençage haut débit dans l'amélioration de la prise en charge des maladies monogéniques." Thesis, Aix-Marseille, 2016. http://www.theses.fr/2016AIXM5062/document.
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La diffusion du séquençage haut débit (ou NGS pour Next Generation Sequencing) représente un tel changement d’échelle par rapport aux méthodes classiques de séquençage que les indications et l’organisation du diagnostic moléculaire s’en trouvent profondément modifiées. Le NGS permet à la fois de raccourcir le temps d’analyse et de rendu de résultat et d'élargir considérablement le nombre de gènes testés. Il promet donc d’augmenter la proportion de diagnostics posés et de faciliter l'identification de nouveaux variants et de nouveaux gènes impliqués en pathologie. Cependant dans tous les cas, il génère une quantité de données importante, données qui doivent être analysées et interprétées à l’aide d’outils bioinformatiques spécifiques.Dans la première partie de ce travail, les stratégies existantes ainsi que les difficultés et les enjeux du séquençage haut débit pour le diagnostic moléculaire des maladies génétiques sont discutés. Dans la deuxième partie, la mise en place et la validation technique de cette approche diagnostique sont décrites au sein du laboratoire de Génétique Moléculaire de la Timone à Marseille et illustrées par trois exemples concrets de diagnostics moléculaires posés grâce à la technique de séquençage à haut débit. Dans le domaine spécifique des maladies rares, ces nouvelles technologies sont porteuses d’un réel espoir pour les patients atteints de maladie génétique, permettant d'améliorer globalement leur prise en charge et d'accélérer les progrès dans le domaine de la rechercheThe diffusion of Next Generation Sequencing (NGS) technologies induces an important change that modifies molecular diagnostics indications and prompts laboratories to re-think their diagnostic strategies, up-to-now based on Sanger sequencing routine. Several high throughput approaches are available from the sequencing of a gene panel, to a whole exome, or even a whole genome. In all cases, a tremendous amount of data are generated, that have to be filtered, interpreted and analyzed by the use of powerful bioinformatics tools.In part 1, existing strategies and the difficulties and challenges of high-throughput sequencing for molecular diagnosis in genetic diseases are discussed. In part 2, the set up and the technical validation of this diagnostic approach in the Molecular Genetics’ Laboratory of the Timone Hospital in Marseille is presented and illustrated by 3 examples of complex diagnostics solved thanks to NGS. NGS promises to shorten significantly the time of analysis and results reporting, and to expand the number of tested genes. It also promises to increase the proportion of positive diagnoses. Finally, the NGS can identify new variants and new genes involved in human pathology, thus will globally improve patient clinical care
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Vining, Nicholas. "Next-generation content creation: an investigative approach." Thesis, 2011. http://hdl.handle.net/1828/3830.
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The rising cost in video game content creation, both in terms of man hours and in terms of monetary dollars, restricts the ability of video game developers to create unique, entertaining content. Motivated by how this cost is a direct result of "next-generation graphics", I am motivated to ask: what would a next-generation content creation tool look like? I investigate the problem by constructing several such tools. In particular, I construct a mesh quilting algorithm for random level generation, a rapid level construction toolkit based on the concept of an architectural blueprint but supporting features such as complex silhouette geometry and roof geometry, and a tool for rapidly painting world textures. I also introduce a new system for accessing barycentric coordinate data from within the fragment shader, which can be used in support of real-time 3D image quilting, more accurate normal interpolation, and texture rendering from within the world painting tool. Some history of video game content creation is discussed, and a roadmap is charted for future development.Graduate
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Alhomoud, Adeeb M., Irfan U. Awan, Disso Jules F. Pagna, and M. Younas. "A Next Generation Approach to Combating Botnets." 2013. http://hdl.handle.net/10454/13626.
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noAs part of a defense-in-depth security solution for domain-controlled enterprise networks, a proposed self-healing system architecture is designed to increase resiliency against botnets with minimal disruption to network services.
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Doucette, Cody. "An architectural approach for mitigating next-generation denial of service attacks." Thesis, 2021. https://hdl.handle.net/2144/42216.
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It is well known that distributed denial of service attacks are a major threat to the Internet today. Surveys of network operators repeatedly show that the Internet's stakeholders are concerned, and the reasons for this are clear: the frequency, magnitude, and complexity of attacks are growing, and show no signs of slowing down. With the emergence of the Internet of Things, fifth-generation mobile networks, and IPv6, the Internet may soon be exposed to a new generation of sophisticated and powerful DDoS attacks.
But how did we get here? In one view, the potency of DDoS attacks is owed to a set of underlying architectural issues at the heart of the Internet. Guiding principles such as simplicity, openness, and autonomy have driven the Internet to be tremendously successful, but have the side effects of making it difficult to verify source addresses, classify unwanted packets, and forge cooperation between networks to stop traffic. These architectural issues make mitigating DDoS attacks a costly, uphill battle for victims, who have been left without an adequate defense.
Such a circumstance requires a solution that is aware of, and addresses, the architectural issues at play. Fueled by over 20 years worth of lessons learned from the industry and academic literature, Gatekeeper is a mitigation system that neutralizes the issues that make DDoS attacks so powerful. It does so by enforcing a connection-oriented network layer and by leveraging a global distribution of upstream vantage points. Gatekeeper further distinguishes itself from previous solutions because it circumvents the necessity of mutual deployment between networks, allowing deployers to reap the full benefits alone and on day one.
Gatekeeper is an open-source, production-quality DDoS mitigation system. It is modular, scalable, and built using the latest advances in packet processing techniques. It implements the operational features required by today's network administrators, including support for bonded network devices, VLAN tagging, and control plane tools, and has been chosen for deployment by multiple networks.
However, an effective Gatekeeper deployment can only be achieved by writing and enforcing fine-grained and accurate network policies. While the basic function of such policies is to simply govern the sending ability of clients, Gatekeeper is capable of much more: multiple bandwidth limits, punishing flows for misbehavior, attack detection via machine learning, and the flexibility to support new protocols. Therefore, we provide a view into the richness and power of Gatekeeper policies in the form of a policy toolkit for network operators.
Finally, we must look to the future, and prepare for a potential next generation of powerful and costly DDoS attacks to grace our infrastructure. In particular, link flooding attacks such as Crossfire use massive, distributed sets of bots with low-rate, legitimate-looking traffic to attack upstream links outside of the victim's control. A new generation of these attacks could soon be realized as IoT devices, 5G networks, and IPv6 simultaneously enter the network landscape. Gatekeeper is able to hinder the architectural advantages that fuel link flooding attacks, bounding their effectiveness.
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(9593063), Li Cheng. "Laboratory Load-Based Testing, Performance Mapping and Rating of Residential Cooling Equipment." Thesis, 2020.
Find full textAbstract:
In the U.S., unitary residential air conditioners are rated using standard AHRI 210/240 that is inadequate to credit equipment with advanced controls and variable-speed components since the ratings are based on results of steady-state laboratory tests. Contrarily, a load-based testing and rating approach is presented in this work that can capture equipment performance with its integrated controls and thermostat responses that is more representative of the field. In this approach, representative building sensible and latent loads are emulated in a psychrometric test facility at different indoor and outdoor test conditions utilizing a virtual building model. The indoor test room conditions are continuously adjusted to emulate the dynamic response of the virtual building to the test equipment sensible and latent cooling rates and the equipment dynamic response is measured. Meanwhile, the inlet temperatures to the test equipment thermostat are independently controlled to track the same virtual building response using a thermostat environment emulator that encloses the test thermostat, that provides typical flow conditions and of which the design and control are presented in this work. Climate-specific cooling seasonal performance ratings can be determined by propagating load-based test results through a temperature-bin method to estimate a seasonal coefficient of performance (SCOP). In addition, a next-generation rating approach is developed that extends load-based testing for performance mapping, such that the SCOP can be obtained using building simulations that incorporate specific building types, climates and an equipment-specific performance map.
In this work, the proposed approaches were implemented to test and rate a variable-speed residential heat pump operating in cooling mode. Trained with results from only 12 load-based test intervals carried out using the test equipment, a quasi-steady-state mapping model was able to map the equipment performance across almost the entire operating envelope within $\pm10\%$ errors and the $R^2$ values were very close to 1. Using the identified performance map, the next-generation SCOP was obtained based on an annual simulation deployed in EnergyPlus, where the map was coupled to a typical single-family building in Albuquerque,NM. Compared to the temperature-bin-based rating, this simulation-based rating is able to comprehensively and appropriately reflect equipment annual field performance associated with a specific building type and climate, as the rating is extended from automated laboratory load-based testing and performance mapping.
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Alsarhan, Ayoub. "Machine Learning Approach for Spectrum Sharing in the Next Generation Cognitive Mesh Network." Thesis, 2011. http://spectrum.library.concordia.ca/7710/1/Alsarhan_PhD_F2012.pdf.
Full textAbstract:
Nowadays, there is an unexpected explosion in the demand for wireless network resources. This is due to the dramatic increase in the number of the emerging web-based services. For wireless computer network, limited bandwidth along with the transmission quality requirements for users, make quality of service (QoS) provisioning a very challenging problem. To overcome spectrum scarcity problem, Federal Communications Commission (FCC) has already started working on the concept of spectrum sharing where unlicensed users (secondary users, SUs) can share the spectrum with licensed users (primary users, PUs), provided they respect PUs rights to use spectrum exclusively. Cognitive technology presents a revolutionary wireless communication where users can exploit the spectrum dynamically. The integration of cognitive technology capability into the conventional wireless networks is perhaps the significant promising architectural upgrade in the next generation of wireless network that helps to solve spectrum scarcity problem.
In this work, we propose integrating cognitive technology with wireless mesh network to serve the maximum number of SUs by utilizing the limited bandwidth efficiently. The architecture for this network is selected first. In particular, we introduce the cluster-based architecture, signaling protocols, spectrum management scheme and detailed algorithms for the cognitive cycle. This new architecture is shown to be promising for the cognitive network. In order to manage the transmission power for the SUs in the cognitive wireless mesh network, a dynamic power management framework is developed based on machine learning to improve spectrum utilization while satisfying users requirements. Reinforcement learning (RL) is used to extract the optimal control policy that allocates spectrum and transmission powers for the SUs dynamically. RL is used to help users to adapt their resources to the changing network conditions. RL model considers the spectrum request arrival rate of the SUs, the interference constraint for the PUs, the physical properties of the channel that is selected for the SUs, PUs activities, and the QoS for SUs.
In our work, PUs trade the unused spectrum to the SUs. For this sharing paradigm, maximizing the revenue is the key objective of the PUs, while that of the SUs is to meet their requirements and obtain service from the rented spectrum. However, PUs have to maintain their QoS when trading their spectrum. These complex conflicting objectives are embedded in our machine learning model. The objective function is defined as the net revenue gained by PUs from renting some of their spectrum. We use a machine learning to help the PUs to make a decision about the optimal size and price of the offered spectrum for trading. The trading model considers the QoS for PUs and SUs, traffic load at the PUs, the changes in the network conditions, and the revenues of the PUs. Finally, we integrate all the mechanisms described above to build a new cognitive network where users can interact intelligently with network conditions.
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Liu, Fa-Jen, and 劉發仁. "A homology-based approach for identifying Plant MicroRNAs from Next-Generation Sequencing Data." Thesis, 2019. http://ndltd.ncl.edu.tw/cgi-bin/gs32/gsweb.cgi/login?o=dnclcdr&s=id=%22107NCHU5105030%22.&searchmode=basic.
Full textAbstract:
碩士國立中興大學
基因體暨生物資訊學研究所
107
MicroRNAs (miRNAs) are short non-coding RNAs with about 22 nt in length. Their main function is to regulate the expression of messenger ribonucleic acids (mRNAs) that can be translated into proteins in organisms. Due to the development of next-generation sequencing (NGS) technology, small RNA sequencing (sRNA-Seq) can be used to help miRNAs prediction. Among the sRNA-Seq-based prediction methods, the reference genome-guided methods express higher precision; on the other hand, most of the genome-free methods utilize the machine learning technology to do prediction, however, the result has a higher false positive rate. This study developed a homology-based approach which is independent of the reference genome to analyze sRNA-Seq data. Previously published sRNA-Seq data of Arabidopsis thaliana were used to test the performance of the new appoach. The results from the new approach were compared with the previously published results by the reference genome-guided method. 83% the miRNA families obtained from the previous study can be identified in the new approach. In addition, the two approaches show similar miRNA expression profiles. We then utilized the new apporach to analyze the miRNAs of Phalaenopsis and Oncidium, and predicted their target genes. In addition, differently expressed miRNAs were identified from different samples and the target genes of most of the differently expressed miRNAs could be predicted. A total of 13 conserved miRNA families, 19 novel miRNA families, and 210 target genes were identified in Phalaenopsis. A total of 17 conserved miRNA families, 1 novel miRNA family, and 35 target genes were identified in the Oncidium. From the miRNA prediction results of Arabidopsis thaliana and the orchids, the feasibility and accuracy of the homology-based approach are demonstrated.Thus this apporach will help to improve the miRNA prediction ability with no reference required, and help researchers to understand the more comprehensive regulatory mechanisms in each organism through miRNA prediction.
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Sigel, Erin Mackey. "A Next-Generation Approach to Systematics in the Classic Reticulate Polypodium vulgare Species Complex (Polypodiaceae)." Diss., 2014. http://hdl.handle.net/10161/9092.
Full textAbstract:
The
Chapter I presents a diploids-only phylogeny of the
Chapter II addresses reported discrepancies regarding the occurrence of
Chapter III examines a case of reciprocal allopolyploid origins in the fern
This dissertation concludes by demonstrating the utility of the allotetraploid
Dissertation
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Parameswaran, Aishwarya. "DNA Encoded Libraries (DEGL) of Glycan Antigens to Detect Antibodies: An Approach Towards Next Generation Functional Glycomics." 2017. http://scholarworks.gsu.edu/chemistry_theses/101.
Full textAbstract:
Structure and functional study of glycans are highly challenging due to the difficulties in analyzing glycans and limited availability of samples for study. These limitations could be resolved by attaching DNA barcode to the glycan, which virtually represent glycan in further application, by increasing the sensitivity of detection by polymerase chain reaction (PCR), requiring minimal samples for analysis. Assuming bigger arena of DNA Encoded Glycan Libraries (DEGL) in future, we propose here a method for uniquely coding all glycans using computer program that can convert the structural information of glycans to DNA barcode. A unique and universal coding for glycans will benefit both synthesis and analysis of DEGLs. As a proof of principle study, a small DNA Encoded Glycan Library (DEGL) of blood and globo series glycan antigen and its application was demonstrated in detecting blood group and breast cancer from plasma.
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Eddyani, M., K. Vandelannoote, Conor J. Meehan, S. Bhuju, J. L. Porter, J. Aguiar, T. Seemann, et al. "A Genomic Approach to Resolving Relapse versus Reinfection among Four Cases of Buruli Ulcer." 2015. http://hdl.handle.net/10454/17297.
Full textAbstract:
YesBackground. Increased availability of Next Generation Sequencing (NGS) techniques allows, for the first time, to distinguish relapses from reinfections in patients with multiple Buruli ulcer (BU) episodes. Methodology. We compared the number and location of single nucleotide polymorphisms (SNPs) identified by genomic screening between four pairs of Mycobacterium ulcerans isolates collected at the time of first diagnosis and at recurrence, derived from a collection of almost 5000 well characterized clinical samples from one BU treatment center in Benin. Principal Findings. The findings suggest that after surgical treatment—without antibiotics—the second episodes were due to relapse rather than reinfection. Since specific antibiotics were introduced for the treatment of BU, the one patient with a culture available from both disease episodes had M. ulcerans isolates with a genomic distance of 20 SNPs, suggesting the patient was most likely reinfected rather than having a relapse. Conclusions. To our knowledge, this study is the first to study recurrences in M. ulcerans using NGS, and to identify exogenous reinfection as causing a recurrence of BU. The occurrence of reinfection highlights the contribution of ongoing exposure to M. ulcerans to disease recurrence, and has implications for vaccine development.
This work was supported by the UBS Optimus Foundation (Zurich, Switzerland) and the Department of Economy, Science and Innovation of the Flemish Government (Belgium). KV was supported by a VLADOC PhD scholarship of VLIRUOS (Belgium).
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Wu, Chih-hsien, and 吳致憲. "Adaptive Load Balancing MDP-based Approach of Two-Dimension Spreading for VSF-OFCDM in Next Generation Cellular Communications." Thesis, 2007. http://ndltd.ncl.edu.tw/handle/14631427024750335633.
Full textAbstract:
碩士朝陽科技大學
資訊工程系碩士班
95
The VSF-OFCDM system has been proposed as the forward link interface for achieving high data rate in 4G mobile communications. VSF-OFCDM allocates orthogonal channelization codes of an OVSF code tree in two-dimension (2D) spreading in the time and frequency domains, but suffers from two disadvantages: moderate utilization and low transmission quality. The moderate utilization is caused by code blocking and the low transmission quality is due to the multicode interference from high channel loading in the time domain of the two-dimension spreading. A trade-off exists between code blocking and multicode interference. Specifically, lower the code blocking the system has, higher the interference it yields. To achieve high utilization while providing high transmission quality becomes the critical issue that should be addressed in 4G VSF-OFCDM. Therefore, in this paper, we propose the Adaptive Load-balancing with Markov decision process based 2D spreading approach (i.e., denoted by ALM) for the purpose. The ALM approach consists of three phases. First, for balancing channel load, the adaptive 2D spreading phase is proposed to select that the 2D spreading combinations are with low channel load and high frequency diversity as the candidates. Second, a dynamic re-combination of a 2D spreading is proposed to decrease channel load while supporting transmission quality from high frequency diversity if the channel load of a time domain code exceeds the defined channel load threshold. Third, for minimizing the code blocking, the cost-based Markov decision process code selection approach is adopted. The MDP phase selects the least cost channelization code as the optimal solution if there are several 2D spreading combinations that satisfy the channel load limitation. In addition, the time complexity of ALM is analyzed. Numerical results indicate that the proposed approach outperforms other approaches in transmission quality ratio, fractional reward loss and the total number of reassignments.
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Blaschikoff, Ludmilla Paixão. "Dogs (Canis lupus familiaris) from the Iberian Peninsula dated to the Chalcolithic period: a genomic approach." Master's thesis, 2019. http://hdl.handle.net/10773/26896.
Full textAbstract:
Os cães existem na Península Ibérica pelo menos desde o Paleolítico Superior;
o resto arqueológico mais antigo data há cerca de 16,000 AP (Erralla, Espanha).
Existem diferentes teorias sobre a origem dos cães na Europa. Estudos
anteriores indicam que os cães podem ter chegado à Europa a partir de uma
população domesticada de lobos oriundos da Ásia Oriental, ou a partir de duas
populações de lobos geneticamente distintas da Eurásia Oriental e Ocidental,
domesticadas independentemente, e que mais tarde, a população de cães da
Eurásia Oriental se espalhou e substituiu parcialmente a população da Eurásia
Ocidental.
Um estudo recente focando na composição genética de 6 cães Ibéricos do
período Mesolítico, sugeriu que uma domesticação local na Península Ibérica
pode ter ocorrido na Europa pré-Neolítica. Considerando o debate mantido
sobre a origem dos cães, é crucial desvendar a composição genética de
populações passadas e periféricas da Europa – usando métodos específicos
para recuperar e analisar o DNA ancestral, de diferentes períodos, a fim de
investigar a origem e a trajetória evolutiva dos cães no seu global.
Nomeadamente, pode revelar-se importante por fornecer dados sobre uma
possível contribuição do lobo Ibérico para a origem dos primeiros cães Ibéricos
e informação genómica potencialmente útil para a detecção de eventos de
hibridação histórica entre o cão e o seu parente selvagem, o lobo Ibérico – uma
subespécie endêmica e atualmente considerada “Em perigo” de extinção. Esta
informação pode ser englobada aquando a definição de medidas de gestão e
conservação futuras para a espécie selvagem lobo Ibérico.
Neste trabalho, uma abordagem genómica (Next Generation Sequencing, NGS)
foi a escolhida para recuperar sequências do genoma mitocondrial (mt) e nuclear
de Canis de três sítios arqueológicos Ibéricos datados do Calcolítico [ca. 5,000-
4,000 anos atrás]: dois cães de Leceia em Oeiras, Portugal; dois cães de
Casetón de La Era em Valladolid, Espanha; e um lobo de Penedo de Lexim em
Mafra, Portugal. Utilizando as ferramentas de bioinformática actuais, esses
genomas foram identificados e compilados. Além disso, para entender a relação
de populações passadas/modernas, construiu-se uma rede filogenética
(baseada num fragmento parcial da região controlo do mtDNA) reunindo 254
sequências de Canis, bem como uma árvore filogenética de 23 mitogenomas de
Canis disponíveis em bases dados públicos.
Embora a recuperação e análise do genoma nuclear sejam um maior desafio se
proveniente de amostras ancestrais, este foi investigado para a identificação do
sexo molecular desses 5 espécimes.
Relativamente ao estudo dos cães pré-históricos da Ibéria, esta é a primeira
tentativa de aplicar com sucesso o método NGS para investigar a sua
composição genética. Neste estudo, foi possível: gerar sequências do genoma
mitocondrial (com 1x a 17x de cobertura) e recuperar entre 0.09% e 3.75% do
genoma nuclear endógeno das 5 amostras do Calcolítico; identificar haplótipos
de DNA mitocondrial e atribuí-los a dois (A e C) dos quatro principais
haplogrupos descritos para os cães (A, B, C e D); gerar dados genómicos de um
lobo Ibérico do Calcolítico que, tanto quanto investiguei, constituem os primeiros
dados genómicos de um espécime de lobo da Ibéria e desta cronologia. Os
resultados mostram que os cães Ibéricos do Calcolítico apresentavam a mesma
frequência de haplótipos do Haplogrupo A (Hg anteriormente presente neste
território, em contraste com as outras regiões da Europa), bem como do
Haplogrupo C (já presente em outras regiões da Europa desde o Paleolítico).Domestic dogs exist in the Iberian Peninsula at least since the Upper Late Palaeolithic; the oldest remain dated to 16,000 BP years old (Erralla, Spain). There are different theories about the origins of European dogs. Previous studies indicated that dogs may arrived in Europe from an Eastern Asia domesticated population of wolves, or that two genetically distinct wolf populations in Eastern and Western Eurasia may have been independently domesticated, and that afterwards the Eastern dog population spread and partially replaced an indigenous Western Eurasian dog population. A recent study focusing in the genetic composition of 6 Mesolithic Iberian dogs reported that a local domestication in the Iberia Peninsula may have occurred in pre-Neolithic Europe. Considering the debated origin of Iberian dogs, it is crucial to unravel the genetic composition of past European peripheral populations - using specific methods to recover and analyse ancient DNA, from different periods in order to further investigate their origins and evolutionary trajectories. Additionally, it may prove important to provide data on a possible contribution of the Iberian wolf to the origin of the first Iberian dogs and genomic information potentially useful for the detection of historical hybridization events between the dog and its wild relative, the Iberian wolf – a subspecies and an endemism currently considered “Endangered”. This information can be included in the definition of future management and conservation measures for the wild Iberian wolf species. In this work, a genomic approach (Next Generation Sequencing, NGS) was carried out to recover mitogenome and nuclear genomic data of Canis from three Iberian archaeological sites dated to the Chalcolithic [ca. 5,000-4,000 years BP], in particular: two dogs from Leceia in Oeiras, Portugal; two dogs from Casetón de La Era in Valladolid, Spain; and one wolf from Penedo de Lexim in Mafra, Portugal. Using the most up-to-date bioinformatic tools, their mitochondrial (mt) and nuclear genomes were sequenced. In addition, to understand the relationship of past/extant populations, a phylogenetic network (based on a partial fragment of the mtDNA control region) comprising 254 Canis sequences, as well as a phylogenetic tree of 23 Canis mitogenomes, publicly available, were constructed. Furthermore, the nuclear genome, although more challenging to recover and analyse from ancient samples, was investigated to molecularly assess the sex of these 5 Canis specimens. Regarding ancient Iberian dogs, this is the first attempt to successfully apply NGS methods to investigate their genomic composition. In this study, it was possible to: generate the draft of mitochondrial genomes (coverages ranged between 1x and 17x) and recover between 0.09% and 3.75% of endogenous nuclear genomic data of these 5 Canis specimens; identify mitochondrial DNA haplotypes and assign those to 2 (A and C) of the four major dog haplogroups described (A, B C and D); generate genetic data from a Chalcolithic wolf - to the best of my knowledge this is the first genomic data available from an Iberian wolf specimen from this chronology. The results shown that the Chalcolithic Iberian dogs had about the same frequency of Haplogroup A (previously present in this territory, but contrasting with other European regions), as well as of the Haplogroup C (already present in other European regions since the Paleolithic).
Mestrado em Ecologia Aplicada
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Martins, Sara Patrícia Monteiro. "A metagenomic approach to identify and characterize wastewater populations." Master's thesis, 2017. http://hdl.handle.net/1822/56115.
Full textAbstract:
Dissertação de mestrado em BioinformaticsWater scarcity and pollution are two main ecological focus nowadays. Knowledge of wastewater composition, regarding microorganisms and pollutants, is of great importance to improve the capacities of the effluent treatment plants (ETP). Advances in Next-generation sequencing (NGS) methodologies allowed for faster, cheaper and more accurate study of microbial communities. Besides being an extremely powerful analysis resource, whole shotgun metagenomic analysis comprises many challenging aspects, regarding the processing and analysis. In the present work a shotgun metagenomic bioinformatics analysis was performed comprising three samples from common ETPs (CETP) and four samples from a petrochemical complex ETPs (wastewaters with low and high salts collected in two distinct timepoints). The samples were sequenced with Illumina® HiSeq, generating paired-end reads with 2x150bp length. The main goals of this project were to evaluate currently available tools, establish a customized bioinformatics pipeline and to extract relevant biological information from the sequenced datasets. There were generated simulated datasets representative of the target data, in order to evaluate the performance of the available bioinformatics tools. Datasets were generated with three coverage levels and were used to test pre-processing, assembly and taxonomic tools. The target datasets, both with and without coverage split, were then subjected to processing and analysis using the pre-defined pipeline. A preliminary functional study was also performed using MG-RAST and MGX. Results from the evaluation of the performance of the bioinformatics tools showed that different tools behave differently in distinct datasets. The pipeline was defined using BayesHammer and Fastq-mcf as pre-processing tools, SPAdes for assembly and MetaPhlAn v2.0 for the taxonomical analysis. The assembly results for the target datasets showed a higher contiguity for high coverage levels and a lower contiguity for low coverage levels, highlighting the differences in microorganisms’ abundance and diversity and its impact during analysis. Taxonomical composition suggests the presence of putative pathogenic and opportunistic microorganisms on two of the CETP datasets (A2 and AKR12). It also suggests a more hostile environment in petrochemical complex ETPs datasets, which is concordant with a higher abundance of defence mechanisms on this datasets. The present results must be accounted to the effluent treatment processes.
A escassez de água e a poluição são dois dos principais problemas ecológicos atualmente. O conhecimento da composição das águas residuais, referente a microrganismos e poluentes, é de grande importância para melhorar as capacidades das estações de tratamento de águas residuais (ETAR). Os avanços nos métodos de sequenciação de nova geração permitiram o estudo mais rápido, barato e preciso de comunidades microbianas. Apesar de ser um meio de análise altamente poderoso, a análise metagenómica por whole shotgun compreende muitos aspetos desafiadores, no que respeita o processamento e a análise. No presente trabalho, uma análise bioinformática de dados metagenómicos de shotgun foi efetuada incluindo três amostras de ETARs comuns e quatro amostras de ETARs de um complexo petroquímico (águas residuais com baixos e altos teores de sais, colhidas em dois momentos distintos). As amostras foram sequenciadas com Illumina® HiSeq, gerando paired-end reads com comprimento igual a 2x150pb. Os principais objetivos deste projeto foram avaliar ferramentas disponíveis atualmente, estabelecer uma pipeline bioinformática personalizada e extrair informação biológica relevante dos datasets sequenciados. Foram gerados datasets simulados representativos dos dados a analisar, de forma a avaliar a performance das ferramentas bioinformáticas disponíveis. Os datasets foram gerados com três níveis de coverage e foram usados para testar ferramentas de pré-processamento, assembly e taxonomia. Os datasets alvo, com e sem divisão por coverage, foram então sujeitos a processamento e análise usando a pipeline pré-definida. Um estudo funcional preliminar foi realizado com MG-RAST e MGX. Os resultados da avaliação da performance das ferramentas bioinformáticas mostraram que diferentes ferramentas comportam-se de forma diferente em datasets distintos. A pipeline foi definida usando BayesHammer e Fastq-mcf como ferramentas de pré-processamento, SPAdes para assembly e MetaPhlAn v2.0 para a análise taxonómica. Os resultados de assembly para os datasets alvo mostraram uma grande contiguidade para altos níveis de coverage e baixa contiguidade para baixos níveis de coverage, realçando as diferenças de abundância e diversidade dos microrganismos e o seu impacto durante a análise. A composição taxonómica sugere a presença de microrganismos potencialmente patogénicos e oportunistas nos dois datasets de ETARs comuns (A2 e AKR12). Sugere também um ambiente mais hostil nos datasets das ETARs do complexo petroquímico, o que é concordante com uma maior abundância de mecanismos de defesa nestes datasets. Os presentes resultados devem ser tidos em conta nos processos de tratamento de águas residuais. Palavras-chave: metagenómica de whole shotgun, sequenciação de nova geração, estação de tratamento de águas residuais.
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Krahn, Elizabeth. "An autoethnographic study of the legacies of collective trauma experienced by Russian Mennonite women who immigrated to Canada after WWII: implications on aging and the next generation." 2011. http://hdl.handle.net/1993/4821.
Full textAbstract:
This thesis explores lifespan and intergenerational trauma effects experienced by Russian Mennonite women who fled from Stalinist Russia during WWII and migrated to Canada, and adult sons or daughters of this generation of women. As an adult child of survivors, I employed an autoethnographic methodology, conducting 1-on-1 interviews with eight women aged 78 to 96, and seven adult children aged 50 to 68. Older women demonstrated a lifelong emphasis on mental strength, faith, and resilience; the marginalization of emotions; evidence of insecure attachment styles; and potential for unresolved trauma to resurface in later life. The majority of adult children experienced attachment and identity issues; their life experiences are viewed through the lens of biological, psychological, familial, cultural (religious) transmission of trauma effects. Results highlight the importance of structural and narrative social work approaches that externalize and contextualize trauma and transform service environments that individualize and/or pathologize lifespan outcomes of trauma.
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Zulu, Lindinkosi Lethukuthula. "Simmulating and prototyping software definednetworking (SDN) using Mininet approach to optimise host communication in realistic programmable networking environment." Diss., 2018. http://hdl.handle.net/10500/26156.
Full textAbstract:
In this project, two tests were performed. On the first test, Mininet-WiFi was used to simulate a
Software Defined Network to demonstrate Mininet-WiFi’ s ability to be used as the Software
Defined Network emulator which can also be integrated to the existing network using a Network
Virtualized Function (NVF). A typical organization’s computer network was simulated which
consisted of a website hosted on the LAMP (Linux, Apache, MySQL, PHP) virtual machine, and
an F5 application delivery controller (ADC) which provided load balancing of requests sent to the
web applications. A website page request was sent from the virtual stations inside Mininet-WiFi.
The request was received by the application delivery controller, which then used round robin
technique to send the request to one of the web servers on the LAMP virtual machine. The web
server then returned the requested website to the requesting virtual stations using the simulated
virtual network. The significance of these results is that it presents Mininet-WiFi as an emulator,
which can be integrated into a real programmable networking environment offering a portable,
cost effective and easily deployable testing network, which can be run on a single computer. These
results are also beneficial to modern network deployments as the live network devices can also
communicate with the testing environment for the data center, cloud and mobile provides.
On the second test, a Software Defined Network was created in Mininet using python script. An
external interface was added to enable communication with the network outside of Mininet. The
amazon web services elastic computing cloud was used to host an OpenDaylight controller. This
controller is used as a control plane device for the virtual switch within Mininet. In order to test
the network, a webserver hosted on the Emulated Virtual Environment – Next Generation (EVENG)
software is connected to Mininet. EVE-NG is the Emulated Virtual Environment for
networking. It provides tools to be able to model virtual devices and interconnect them with other
virtual or physical devices. The OpenDaylight controller was able to create the flows to facilitate
communication between the hosts in Mininet and the webserver in the real-life network.Electrical and Mining Engineering
46
Zulu, Lindinkosi Lethukuthula. "Simulating and prototyping software defined networking (sdn) using mininet approach to optimise host communication in realistic programmable networking environment optimise host communication in realistic programmable networking environment." Diss., 2019. http://hdl.handle.net/10500/25780.
Full textAbstract:
This is a Masters student Final DissertationIn this project, two tests were performed. On the first test, Mininet-WiFi was used to simulate a Software Defined Network to demonstrate Mininet-WiFi’ s ability to be used as the Software Defined Network emulator which can also be integrated to the existing network using a Network Virtualized Function (NVF). A typical organization’s computer network was simulated which consisted of a website hosted on the LAMP (Linux, Apache, MySQL, PHP) virtual machine, and an F5 application delivery controller (ADC) which provided load balancing of requests sent to the web applications. A website page request was sent from the virtual stations inside Mininet-WiFi. The request was received by the application delivery controller, which then used round robin technique to send the request to one of the web servers on the LAMP virtual machine. The web server then returned the requested website to the requesting virtual stations using the simulated virtual network. The significance of these results is that it presents Mininet-WiFi as an emulator, which can be integrated into a real programmable networking environment offering a portable, cost effective and easily deployable testing network, which can be run on a single computer. These results are also beneficial to modern network deployments as the live network devices can also communicate with the testing environment for the data center, cloud and mobile provides. On the second test, a Software Defined Network was created in Mininet using python script. An external interface was added to enable communication with the network outside of Mininet. The amazon web services elastic computing cloud was used to host an OpenDaylight controller. This controller is used as a control plane device for the virtual switch within Mininet. In order to test the network, a webserver hosted on the Emulated Virtual Environment – Next Generation (EVENG) software is connected to Mininet. EVE-NG is the Emulated Virtual Environment for networking. It provides tools to be able to model virtual devices and interconnect them with other virtual or physical devices. The OpenDaylight controller was able to create the flows to facilitate communication between the hosts in Mininet and the webserver in the real-life network
The University of South Africa The University of Johannesburg
College of Engineering, Science and Technology
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Zulu, Lindinkosi Lethukuthula. "Simulating and prototyping software defined networking (SDN) using Mininet approach to optimise host communication in realistic programmable networking environment." Diss., 2018. http://hdl.handle.net/10500/26218.
Full textAbstract:
In this project, two tests were performed. On the first test, Mininet-WiFi was used to simulate a
Software Defined Network to demonstrate Mininet-WiFi’ s ability to be used as the Software
Defined Network emulator which can also be integrated to the existing network using a Network
Virtualized Function (NVF). A typical organization’s computer network was simulated which
consisted of a website hosted on the LAMP (Linux, Apache, MySQL, PHP) virtual machine, and
an F5 application delivery controller (ADC) which provided load balancing of requests sent to the
web applications. A website page request was sent from the virtual stations inside Mininet-WiFi.
The request was received by the application delivery controller, which then used round robin
technique to send the request to one of the web servers on the LAMP virtual machine. The web
server then returned the requested website to the requesting virtual stations using the simulated
virtual network. The significance of these results is that it presents Mininet-WiFi as an emulator,
which can be integrated into a real programmable networking environment offering a portable,
cost effective and easily deployable testing network, which can be run on a single computer. These
results are also beneficial to modern network deployments as the live network devices can also
communicate with the testing environment for the data center, cloud and mobile provides.
On the second test, a Software Defined Network was created in Mininet using python script. An
external interface was added to enable communication with the network outside of Mininet. The
amazon web services elastic computing cloud was used to host an OpenDaylight controller. This
controller is used as a control plane device for the virtual switch within Mininet. In order to test
the network, a webserver hosted on the Emulated Virtual Environment – Next Generation (EVENG)
software is connected to Mininet. EVE-NG is the Emulated Virtual Environment for
networking. It provides tools to be able to model virtual devices and interconnect them with other
virtual or physical devices. The OpenDaylight controller was able to create the flows to facilitate
communication between the hosts in Mininet and the webserver in the real-life network.Electrical and Mining Engineering
M. Tech. (Electrical Engineering)