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Developing a Computational Pipeline for Detecting Multi-Functional Antibiotic Resistance Genes in Metagenomics DataDang, Ngoc Khoi 09 June 2022 (has links)
Antibiotic resistance is currently a global threat spanning clinical, environmental, and geopolitical research domains. The environment is increasingly recognized as a key node in the spread of antibiotic resistance genes (ARGs), which confer antibiotic resistance to bacteria. Detecting ARGs in the environment is the first step in monitoring and controlling antibiotic resistance. In recent years, next-generation sequencing of environmental samples (metagenomic sequencing data) has become a prolific tool for the field of surveillance. Metagenomic data are nucleic acid sequences, or nucleotides, of environmental samples. Metagenomic sequencing data has been used over the years to detect and analyze ARGs. An intriguing instance of ARGs is the multi-functional ARG, where one ARG encodes two or more different antibiotic resistance functions. Multi-functional ARGs provide resistance to two or more antibiotics, thus should have evolutionary advantage over ARGs with resistance to single antibiotic. However, there is no tool readily available to detect these multi-functional ARGs in metagenomic data. In this study, we develop a computational pipeline to detect multi-functional ARGs in metagenomic data. The pipeline takes raw metagenomic data as the input and generates a list of potential multi-functional ARGs. A plot for each potential multi-functional ARG is also created, showing the location of the multi-functionalities in the sequence and the sequencing coverage level. We collected samples from three different sources: influent samples of a wastewater treatment plant, hospital wastewater samples, and reclaimed water samples, ran the pipeline, and identified 19, 57, and 8 potentially bi-functional ARGs in each source, respectively. Manual inspection of the results identified three most likely bi-functional ARGs. Interestingly, one bi-functional ARG, encoding both aminoglycoside and tetracycline resistance, appeared in all three data sets, indicating its prevalence in different environments. As the amount of antibiotics keeps increasing in the environment, multi-functional ARGs might become more and more common. The pipeline will be a useful computational tool for initial screening and identification of multi-functional ARGs in metagenomic data. / Master of Science / Antibiotics are the drug to fight against the infection of bacteria. Since the first antibiotic was discovered in 1928, many antibiotic drugs have been developed. At the same time, scientists discovered many genes responsible for the resistance of antibiotic drugs. Nowadays, antibiotic resistance is a global threat. Detecting antibiotic resistance genes in the environment is the first step toward monitoring and controlling antibiotic resistance. In recent years, next-generation sequencing has been widely used to get the DNA sequence from the environment. Metagenomics analysis has been used over the years to detect and analyze ARGs. In the literature, it has been reported that a single gene could carry two parts of sequences corresponding to two different ARGs, thus conferring resistance to two different antibiotics. This fusion might have some evolutionary advantages. In this study, we developed a novel computational tool to detect multi-functional ARGs. We collected data from three sources: the treatment plant water, the hospital wastewater, and the reclaimed water, and identified 19, 57, and 8 potential bi-functional ARGs in each source, respectively. After we manually inspected the result, we found three most likely bi-functional ARGs. We also found one bi-functional ARG that appears in all three datasets. The gene is responsible for aminoglycoside and tetracycline resistance. The tool will serve as the initial screening step to detect multi-functional ARGs.
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Portable landscapes: flexibility and customization associated with temporary landscapesSickmann, Jared January 1900 (has links)
Master of Landscape Architecture / Department of Landscape Architecture/Regional and Community Planning / Howard D. Hahn / Cities and towns across the world are in a dynamic state of change, and therefore, becoming responsive to new and innovative approaches to creating and restoring public spaces. These new approaches address the need for flexible, multifunctional spaces in order to adapt to and accommodate the changing demands and unexpected circumstances that occur within the city (Wall 1999, Temel 2006, Gehl 2011). Temporary landscapes, or site specific, time-limited designs of open space, have become an emerging approach to improving public spaces. These small scale projects provide unique experiences and offer a laboratory for experimentation where new, innovative ideas can be tested (Lydon 2012, Sargin and Savas 2012, Temel 2006).
The idea of flexibility and the need for multifunctional spaces are explored through the following report by investigating how an innovative approach involving temporary landscapes can enhance streetscape quality and offer a variety of public activities. First, I developed a deeper understanding of temporary landscapes in order to identify the transition in approach to urban design from focusing on permanence to temporary, and express the importance of temporality in urban design. A design matrix exploring programmatic options and customizable design features was established through an extensive literature review and case study analysis.
Through the application process, I explored the regulatory process involved in implementing a temporary landscape intended for the Aggieville Business District in Manhattan, Kansas. This procedure involved a review of the city's ordinances and liability concerns, designing a portable landscape, and constructing a prototype to be deployed off-street until approval is gained. The results from this project provide field evidence to support recommendations for future design iterations for portable landscapes that increase pedestrian comfort and support an expanded range of activities for public spaces. Prototypes of different design iterations and replications can also serve as future projects for the College of Architecture, Planning, and Design at Kansas State University. Ultimately, this project will begin a critical discussion of the future role of temporary landscapes in cities that are in a dynamic state of change.
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Promote the Development of Kaohsiung City and Competitive Strategies after Cross-strait in accession to the WTO The Exploitation of Kaohsiung Multi-functional Commerce & Trade ParkYang, Cheng-Yuan 27 August 2003 (has links)
This paper was applied on the methods of ¡§Interactive Management¡]IM¡^ and Nominal Group Technique¡]NGT¡^¡¨. According to the NGT twice meetings, there are 10 strategies that can improve the development of Kaohsiung City.
The APROC plan was authorized by the Executive Yuan on June, 1995. Kaohsiung city government was assigned to renew urban land at Kaohsiung Multi-functional Commerce & Trade Park first on June, 1996.
From the study, the researcher realizes the advantages of importance, background and exploitation problem. Landlords, investors and Kaohsiung city government accorded in this exploitation plan or not that are based on understanding, negotiation and communication. Meanwhile, it was hard to break out in Three Links which have made investors lack of confidence. It makes many obstacles in improving the development of Kaohsiung city after Cross-strait in accession to the WTO. Therefore, it is necessary to explore moreover.
This paper has utilized literary reviews about Kaohsiung Multi-functional Commerce & Trade Park and interviews to collect data.¡@According to the report about ¡§Cross-strait in WTO¡¨, it is also helpful to understand the pro. Eventually, these suggestions from our study, sincerely hope, could be useful in formulating the strategies and regulations of Kaohsiung city government.
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Polyfunkční dům Kutná Hora / Multifunctional House in Kutna HoraVrba, Jiří January 2014 (has links)
The master´s thesis is focused on the preparation and design of project documentation of the multi-functional building. The building is designed on the corner of Sportovců and Waldhauserova streets in Kutná Hora. The concept of the building respects the territorial plan of the city and complements the existing buildings. The building has one underground and four floors. There is basement, two shops and fourteen flats. The building is designed from construction system Vapis.
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Rehabilitace prostoru bývalých Jaselských kasáren v Brně / Rehabilitation Former Jaselsky Barracks Area in BrnoJuráň, Petr January 2012 (has links)
Multifunctional building Jocelyn is set in earlier studies on the proposed urban site Jeselských barracks in Brno, bounded by streets Štefánikova, Staňkova and new streets stretching Roast. The concept of construction within the meaning of form and function is strictly subordinate to his place near the city center. Economically advantageous feature object representing housing, shops, cafes, restaurants, offices, underground parking. The building is divided vertically into two zones: commercial and residential. The dominant number twelve floors is derived from a corner position of the object. Hanging the height of the building directing urban streets rasterization, creating public spaces of different levels. The material object is perforated for convenient access, views and culture connected with the proposed use of the adjacent park. The building is designed as a monolithic skeleton on bored piles with a facade of facework. Ceiling structure consists of a monolithic reinforced concrete slab ceiling with integrated cooling and heating of rooms tempered by the reinforced concrete core.
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Development of Constituents for Multi-functional Composites Reinforced with Cellulosic Fibers / Utveckling av beståndsdelar för multifunktionella kompositer förstärkta med cellulosafibrerAl-Maqdasi, Zainab January 2019 (has links)
Bio-basedcomposites are being increasingly used in applications where weight saving,and environmental friendliness is as important as structural performance. Obviously, bio-based materials have their limitations regarding durability and stability of the properties,but their potential in use for advanced applications can be expanded if they were functionalized and considered beyond their structural performance. Multifunctionalityincomposites can be achieved by modifyingeither of the composite constituents at different levelsso that they can perform energy-associated roles besides their structural reinforcement in the system. For the fibers, this can be done at the microscale by altering theirmicrostructure during spinning process or by applying functional coatings. As for the matrix, it is usually done by incorporating additives that can impart the required characteristics to the matrix. The nano-sized additives that mightbe considered for this objective are graphene and carbon nano-tubes. A big challenge with such materials is the difficulty to reachthe dispersionstate necessary for formation ofstable network to overcome the percolation threshold for conductivity. However, once the network is formed, the composite can have improved mechanical performance together with one or more of the added functionalities such as barrier capabilities,thermal and/or electrical conductivities or electromagnetic interference ability. Enormous work has been done to achieve the functionality incomposites produced with special care in laboratories. However, when it comes to mass production, it is both cost and energy inefficient to use tedious,complex methods for the manufacturing. Hence there is a need to investigate the potential of using scalable and industrial-relevant techniques and materials with acceptable compromise between cost and properties. The work presented in this thesis is performedwithin two projects aiming to achieve functional composites based on natural and man-made cellulosic fibers suitable for industrial upscaling. Conductive Regenerated Cellulose Fibers (RCFs) were produced by coating them with copper by electroless coating process using commercial materials. On the other hand, commercial masterbatches based on Graphene Nano-Platelets (GNPs) were used to produce wood polymer composites (WPC) with added multifunctionality by melt extrusion process. The process is one of the conventional methods used inpolymerproductionand needsno modifications for processingfunctional composites. Both materials together can be used to produce hybrid functional composites. The incorporation of the GNP into HDPE has resulted in improvement in the mechanical propertiesof polymer as well as composite reinforced with wood fibers. Stiffness has increased to a large extent while effect on the strength was less pronounced(>100% and 18% for stiffness and strength at 15%GNP loading). The enhancement of thermal conductivityat higher graphene loadingswas also observed. Moreover, time-dependent response of the polymer has also been affected and the addition of GNP has resulted in reduced viscoplastic strains and improved creep behavior. The copper-coated cellulose fibers showed a significant increasein electrical conductivity(<1Ω/50mm of coated samples) and a potential in use as sensor materials. However, these results come with the cost of reduction in mechanical properties of fibers (10% and 70% for tensile stiffness and strength, respectively) due to theeffect ofchemicals involved in the process.
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Gramática de formas e o mobiliário modular multifuncional : um estudo de casoSchreiner, Fernanda Reis January 2009 (has links)
Esta pesquisa relaciona a teoria da Gramática de Formas (STINY;GIPS, 1972) com os princípios de modulação (HUANG, 2000), para subsidiar um método de antecipação das alternativas de composição capaz de prever a intervenção do usuário. O objeto de investigação, o móvel Vertibral, projetado por Joseph Keenan, é um conjunto de quatro módulos, compostos por 12 requadros lineares de madeira articulados permitindo a interpenetração (WONG,1998) para arranjo entre os módulos. A pesquisa baseia-se na recuperação da gênese do projeto Vertibral a partir de um modelo teórico (associação entre Gramática de Formas e modulação), e seguiu as seguintes etapas: análise do vocabulário do objeto da investigação; identificação e quantificação das relações espaciais possíveis entre dois módulos com a organização de matrizes; exercício de geração de regras formais e arranjos a partir das 232 relações espaciais quantificadas, em relação ao solo quantificadas; e, por último, comparação dos arranjos gerados por participantes do experimento de usabilidade, do tipo Co-discovery (KEMP;GELDEREN, 1996 e DUMAS;REDISH,1993), com relações espaciais quantificadas. A determinação de um método baseado nas etapas deste estudo de caso pode prever a multifuncionalidade para a concepção de um objeto, como o mobiliário. / This research associates the Shape Grammar theory (STINY; GIPS, 1972) to modulation principles (Huang, 2000) as to structure a method for predicting the user’s intervention in modular furniture arrays. The research object, the furniture Vertibral, designed by Joseph Keenan, is constituted by a set of four modules, consisting of 12 wood articulated linear frameworks allowing interpenetration (WONG, 1998) for modules arrangement. The research departs from the retrieval of the Vertibral design principles and follows four steps model: a)object’s vocabulary analysis; b)identification and measurement of possible spatial relationships between two modules with matrices organization; c) generation exercise of formal rules and arrays from 232 computed spatial relations with ground plane reference; and d) comparison of produced arrays made for a usability experiment, according to Co-discovery method (KEMP; GELDEREN, 1996 and DUMAS;REDISH, 1993), with spatial relationships computed. The four stages method seems to have lead to a very high degree of success in creating reliable proxys for multi-functional furniture design.
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Exploring the role of multi-functional solutions when planning for climate change : A case study of stormwater management in a Swedish cityHolgerson, Line January 2015 (has links)
Managing stormwater sustainably in the face of extreme weather events has increasingly been recognized as a strategy for climate adaptation in the urban planning context. Sustainable stormwater management intends to reduce urban vulnerability while ensuring the overall sustainability and robustness of future cities. To add to the emerging research field of green infrastructure, the objective of the study is to explore the role of multi-functional solutions as a climate change response in urban planning and development. This study has been driven by an inductive research process and draws on empirical data collection through workshops and interviews with City Hall officials in Motala City. The study concludes that despite the lack of preventative planning to anticipate climate change, city renewal and urban development of Motala City presented a window of opportunity to implement potential multi-functional stormwater solutions in the urban environment through urban planning. Further, increased focus on internal and external collaboration through the process of envisioning the future of the city have enabled new forms of governance and facilitated arenas for public acceptance and an integrative planning-approach. Lastly, discourses on attractiveness enabled greenery to be viewed from a social, economic and environmental perspective, supporting multi-functional stormwater solutions as a strategy for climate adaptation and urban sustainability.
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Multi-Functional Composite Design Concepts for Rail Vehicle Car BodiesWennberg, David January 2013 (has links)
Structures and material combinations, tailored for multiple purposes, are within the reach of vehicle manufacturers. Besides reducing the environmental impact of the transportation sector these multi-functional structures can reduce costs, such as development, manufacturing and maintenance, and at the same time offer improved comfort to the passengers. This thesis sets out to develop multi-functional design algorithms and evaluate concepts for future composite high speed train car bodies with the objective of optimising the amount of mass needed to fulfil all functions of the structure. In a first step complete composite car bodies were developed, optimised and evaluated based on global stiffness requirements and load cases. The knowledge gained in this step was used as requirements for the strength and stiffness of panels during the continued development of the multi-functional optimisation which, besides strength and stiffness, later also considers sound transmission, thermal insulation, geometric restrictions, manufacturability and fire safety. To be able to include fire safety in the analysis, a method for simulating the high temperature response of layered composite structures was needed, and developed. Significant weight reductions are proven when utilising carbon fibre in the load carrying structure of the vehicle, on component level as high as 60%. Structures can be made significantly thinner when using the algorithms developed in this thesis and wall thickness is reduced by 5-6 cm. Analysis carried out and extensive literature surveys also suggest significant cost savings in manufacturing, maintenance and use-phase, even thou the raw material cost can be significantly higher as compared to the conventional steel or aluminium alternatives. Results from drive cycle simulations showed that the benefit, with respect to reduced energy consumption, is in the range of 0.5-0.8% per reduced weight percentage, comparable to both automotive and air applications. The algorithms and methods established in this thesis can be directly applied for the development and analysis of future high speed train car bodies. / <p>QC 20130521</p>
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Mulity-functional offshore windfarm impact local fishery economical using system dynamics approach‐the case study of Chang Hua Coastal Industrial ParkSyue, Yun-long 12 August 2009 (has links)
The construction of traditional large-scale central power plants and the extension of power lines in Taiwan have tremendous difficulties in terms of land acquisition and environmental protection for a long time. In addition, one potential risk of energy supply is that over 95% of energy source is imported overseas. Therefore, the most important goal of Taiwan energy policy is to cut down the amount of energy import. To achieve the goal, it is important to explore innovatively local energy source by developing renewable and clean energy. Around the available renewable energy technologies, wind power technique is the most mature one in addition to hydraulic power generation. However due to limited land resources and restrictive regulations, it is expected that wind farm development in Taiwan can only be located offshore, instead of inland. Besides, a multi-functional wind farm site, which involves ocean farm ranch, is desirable to bring mutual benefits for both developers and local stake holders.
The current study has used System Dynamics(SD) to analyze the influence of Multi-functional offshore wind farm on economic. We discuss the change of fish catch with building offshore wind farm¡Aand the change of economic output in open ocean with offshore wind farm combine marine ranching. It is therefore easy for the decision makers to comprehend the economical benefit difference if an offshore multi-functional wind farm were to develop in the future. The result of this study is building offshore wind farm will reduced the fishing revenue in a short time¡Abut the total fishing revenue will increased in a long time. The Multi-functional offshore wind farm has better economic output than offshore wind farm.
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