This thesis explores the potential future of medieval churches beyondtheir original function, investigating the transformation of sacral elementsand spaces.Through a case study of the municipality of Vadstena, located in thelandscape of Östergötland, my thesis examines the current state of theparish in Vadstena and its eight medieval churches scattered throughoutthe countryside. As Christianity and the church have had a significantimpact on Vadstena’s history, hosting a former monastery from the 14thcentury and its connected church, the Vadstena monastery church,the town has become a popular destination for tourists interested inexploring religious and historical sites. However, the smaller churches inthe area are scarcely used and struggle to receive proper maintenance andfunding. This raises questions about their survival and the possibility ofrepurposing them. The focus of the thesis is on one of these churches, theÖrberga church, which dates back to the 12th century. My design projectproposes a transformation of the church’s appearance and function,creating a new establishment that caters to traveling pilgrims and regulartourists. The project draws inspiration from former monasteries in thearea and employs the practice of Spolia, a historical method of reuse,to preserve and repurpose parts of the church’s structure into the newadditions on the site.

In a parameterized collaboration design, one views software as a collection of components that play specific roles in interacting, giving rise to collaborative behavior. From this perspective, collaboration designs revolve around reusing collaborations that typify certain design patterns. Unfortunately, verifying that active, concurrently executing components obey the synchronization and communication requirements needed for the collaboration to work is a serious problem. At least two major complications arise in concurrent settings: (1) it may not be possible to analytically identify components that violate the synchronization constraints required by a collaboration, and (2) evolving participants in a collaboration independently often gives rise to unanticipated synchronization conflicts. This work presents a solution technique that addresses both of these problems. Local (that is, role-to-role) synchronization consistency conditions are formalized and associated decidable inference mechanisms are developed to determine mutual compatibility and safe refinement of synchronization behavior. More specifically, given generic parameterized collaborations and components with specific roles, mutual compatibility analysis verifies that the provided and required synchronization models are consistent and integrate correctly. Safe refinement, on the other hand, guarantees that the local synchronization behavior is maintained consistently as the roles and the collaboration are refined during development. This form of local consistency is necessary, but insufficient to guarantee a consistent collaboration overall. As a result, a new notion of global consistency (that is, among multiple components playing multiple roles) is introduced: causal process constraint analysis. A method for capturing, constraining, and analyzing global causal processes, which arise due to causal interference and interaction of components, is presented. Principally, the method allows one to: (1) represent the intended causal processes in terms of interactions depicted in UML collaboration graphs; (2) formulate constraints on such interactions and their evolution; and (3) check that the causal process constraints are satisfied by the observed behavior of the component(s) at run-time. / Ph. D.

Design reuse is an approach in which the creation of new designs is based on the identification of previously employed solutions and the incorporation of those into new contexts. This notion has been extensively studied especially by software engineers. This research seeks to support the reuse of design knowledge in the Human-Computer Interaction (HCI) community in creating new designs as it is generally argued that reuse has the potential to reduce development time and costs. Efforts to reuse design elements in HCI, often in the form of design patterns, are slowly emerging. This work seeks to facilitate the reuse of design knowledge in the form of claims. To achieve this goal, the notion of claim relationships—descriptions of connections between claims that emerge in design—is introduced as a mechanism to facilitate reuse. Claims relationships can be used to connect a collection of reusable claims so that they can be searched, understood, tailored, and integrated into new designs. A method for how to use the relationships is presented to aid in the creation of scenarios. Through a series of studies starting from the use of relationships to locate and reuse claims to the use of cards sets incorporating images and rationale for storyboards, the potential for relationships is demonstrated. These works inform the design and evaluation of a storyboarding tool called PIC-UP. PIC-UP is introduced as an example of how relationships can be utilized in the creation of storyboards made of reusable artifacts in the form of claims. Studies of PIC-UP position the tool as one that enables the reuse through the use of a storyboarding guide and social navigation by collecting and sharing claims. It shows potential in aiding novice and non-designers and can serve as a communication tool. / Ph. D.

Incorporating computers into daily K-12 classroom teaching promises to benefit student learning, and improve teaching practice substantially. Computer enhanced curricula may enable more teachers to create exploratory and inquiry based lessons, but in most cases supporting software have only been realized as practice tools for specific rote learning skills. Drills do little to help students develop higher-order reasoning and problem-solving skills. With more computers in the classroom, the assumption was that computers would be integrated into curricula with a high usage of educational software, but research suggests that this assumption has not been borne out (Powell & Okey, 1994; Tyack & Cuban, 1995). Our general argument is that systems whose usability characteristics have been designed to meet teachers" needs and that can be easily tailored to meet specific teaching objectives are more likely to be incorporated into everyday teaching practices. One type of computer-based activity that enables teachers to engage students in exploratory learning is an educational simulation. Many educational software packages that build simulations have limited usability because they have unmodifiable, limited modifiable or difficult-to-modify functionality. Still others are useful, but are too expensive for many schools to afford. These packages fall short of achieving the ultimate goal of providing useful classroom simulation technology " providing teachers with the option of building simulations from scratch or reusing existing simulations by adapting their functionality. Because teachers have limited time to learn new technology or develop new simulations, this research focused on developing a new framework that would help teachers create easily adaptable and reusable customized educational materials, encouraging them to use these materials to build and extend simulations in collaboration with their students. We began our study by analyzing the currently available tools for visual construction of educational simulations; we used the results of these analyses to develop an alternative environment"SimBuilder. This environment was designed to address the general usability and programming style issues observed in our analysis of other tools. A minimalist self-study tutorial was designed to support rapid start-up and use of the SimBuilder. Through a comparative analysis using a state-of-the-art environment (AgentSheets) that collected a wide range of quantitative and qualitative measures of learning, programming style, usability, motivation, and strategies for code reuse, we determined that SimBuilder offers an improved environment for teachers to construct educational simulations. / Ph. D.

Groundwater plays a fundamental role in water resource sustainability in Virginia (USA), but overpumping has caused significant declines in the potentiometric surface in the Potomac Aquifer System (PAS). With water levels falling, communities are at risk of wells running dry, saltwater intrusion, and land subsidence. The Sustainable Water Initiative for Tomorrow (SWIFT) project is an aquifer long-term replenishment (ALTR) project that uses continuous recharge into the multi-layered confined aquifer system to restore the potentiometric surface over space and time and increase storage in the system. The SWIFT Research Center (SWIFT-RC) is a 1 million gallon per day (MGD) demonstration facility in Suffolk, Virginia that recharges the PAS through a multi-screen well. Addressing research questions about the impact of continuous, sustained recharge on aquifer systems is crucial to the long-term sustainability of an ALTR project. Quantifying how flow moves through the multi-layered system is necessary to communicate travel times and water quality impacts on the aquifer system. This work uses injectate as an intrinsic tracer, an in-situ flowmeter, and a bromide tracer test to evaluate how flow is distributed through the eleven screens in the recharge well and to assess how flow distribution changes over time. Typically, flow distribution in multi-screen wells is estimated only once over the length of a project and assumed to remain constant for modeling purposes; by measuring flow distribution using multiple methods over the course of the project, this work shows that flow distribution is not constant. In future ALTR projects, developing a consistent and robust monitoring plan to use injectate as an indicator of movement through the aquifer system, paired with other methods to monitor changes in flow distribution, will be a critical part of effectively evaluating how flow moves through the groundwater system. / Doctor of Philosophy / Groundwater plays a fundamental role in water resource sustainability in Virginia (USA), but overpumping has left the Potomac Aquifer System (PAS) depleted. With water levels falling, communities are at risk of wells running dry, adverse water quality changes, and even changes to the land surface due to subsurface settling. The Sustainable Water Initiative for Tomorrow (SWIFT) project is an aquifer long-term replenishment (ALTR) project that uses continuous recharge into the deep aquifer system to restore water levels and increase storage in the system. The SWIFT Research Center (SWIFT-RC) is a 1 million gallon per day (MGD) demonstration facility in Suffolk, Virginia that recharges the PAS through a multi-screen well. Addressing research questions about the impact of continuous, sustained recharge on aquifer systems is crucial to the long-term sustainability of an ALTR project. Quantifying how flow moves through the multi-layered system is necessary to communicate travel times and water quality impacts on the aquifer system. This work uses multiple methods to evaluate how flow is distributed through the eleven screens in the recharge well and to assess how flow distribution changes over time. Typically, flow distribution in multi-screen wells is estimated only once over the length of a project and is assumed to remain constant for modeling purposes; by measuring flow distribution using multiple methods over the course of the project, this work shows that flow distribution is not constant. In future ALTR projects, developing a consistent and robust monitoring plan to use recharge water itself as an indicator of movement through the aquifer system, paired with other methods to monitor changes in flow distribution, will be a critical part of effectively evaluating how flow moves through the groundwater system.

Learning objects (LO) reuse is one topical area in instructional design that is gaining popularity in the education economy. It hinges on high hopes and promises to transform how learning occurs in the information age. This study attempted to identify and interrogate the core characteristics of reusable learning objects and conceptualize them as innovations in the curriculum development process. The goal was to synthesize existing knowledge on learning objects, weave streams of literature and research to focus on core arising issues, and then develop an instructional design tool that can help learners easily and effectively find reusable learning objects. The learning objects could be categorized and deconstructed to the levels of their instructional design transformations with regard to macro and micro-level reusability. The researcher used combinatorial developmental research with integrative literature review methodologies to design and develop a metadata management tool. This study involved an in depth review of literature on learning objects, reusable learning objects and their associated metadata management schemes through the integrative literature review approach. Results and data from the integrative literature review were then utilized to design and develop a tool addressing meta-tagging schemes, metadata management, search, and access of learning objects. The researcher identified characteristics of learning objects within the reuse process and discussed best practices, reuse procedures and modeling, based on the analysis of existing cases such as the Open-Knowledge-Initiative (OKI) projects to aid in the tool development. Integrative analysis running concurrently with the development process allowed for rigorous identification and alignment of key factors in the learning objects reuse universe. If fully developed, the metadata management tool could contribute to effective metadata management for learning objects often reused by learning designers, deliverers, and consumers. / Doctor of Philosophy / Learning Objects (LO) reuse is gaining popularity in the field of instructional design. This is because it could transform how learning occurs in today's information age. In this study, I outlined the important characteristics of reusable learning objects and set them up as creative and re-creative products in the curriculum development process. My goal was to combine and reproduce existing literature on LOs that would allow me to develop an instructional design tool to help learning content designers, deliverers, and consumers to easily tag, search, then find reusable learning objects. I reviewed literature on learning objects, reusable learning objects and their associated metadata management schemes then used this data to design and develop the tool addressing meta tagging schemes, metadata management, search, and accessibility of learning objects. The tool allows LO categorization and deconstruction to the largest and smallest granular levels of their instructional reusability. I combined a developmental research method with an integrative literature review method to design and develop the prototype of a tool known as metadata management tool (mmt) for reusable learning objects. If successful, the metadata management tool developed could contribute to an effective metadata management for learning objects often reused by learning designers, deliverers, and consumers.

As climate change exacerbates water scarcity and alters available water and fertilizer resources, it is vital that take appropriate measures to ensure sustainable treatment of water, wastewater, and other waste streams that are protective of public health and support recovery and reuse of water and nutrients. The overarching theme of this dissertation is the advancement of next-generation DNA sequencing (NGS) and computational tools for achieving these goals. A suite of relevant fecal and environmental opportunistic pathogens are examined using both culture-based and NGS-based methods. Of particular concern to this research was not only the attenuation and inactivation of pathogens, but also ensuring that optimal treatment approaches reduce antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Key systems that were the focus of this effort included nutrient reuse (wastewater-derived biosolids and cattle-derived manure), water reuse, and drinking water systems disrupted by a major hurricane. A field study was carried out to survey a suite of pathogens from source-to tap in six small drinking water systems in Puerto Rico six months after Hurricane Maria. The study revealed that pathogenic Leptospira DNA was detected in all systems that were reliant on surface water. On the other hand, Salmonella spp. was detected in surface and groundwater sources and some distribution system waters both by culture and PCR. The study provided comparison of molecular-, microscopic-, and culture-based analysis for pathogen detection and highlighted the need for disaster preparedness for small water systems, including back-up power supply and access to chlorination as soon as possible after a natural disaster. A second field-study examined wastewater derived solids across an international transect of wastewater treatment plants in order to gain insight into the range of ARG concentrations encountered. It was found that, while total ARGs did not vary between treatment or continent of origin, clinically-relevant ARGs (i.e., ARGs encoding resistance to important classes of antibiotics used in humans) were significantly higher in solids derived from Asian wastewater treatment plants. Estimated loading rates of ARGs to soil under a scenario of land application were determined, highlighting in all cases that they are orders of magnitude higher than in the aqueous effluent. Livestock manure, derived from control cattle and cattle undergoing typical antibiotic treatment, and corresponding composts were also evaluated as common soil amendments in a separate study. In this study, the amendments were applied to two soil types in a greenhouse setting, in order to compare the resulting carriage of ARGs on a root (radish) versus leafy (lettuce) vegetable. Remarkably, radishes were found to harbor the highest relative abundance of total ARGs enumerated by metagenomics, even higher than corresponding soils or manures. Although the total microbial load will be lower on a harvested vegetable, the results suggest that the vegetable surface environment can differentially favor the survival of ARBs. The role of wastewater and water reuse treatment processes in reducing ARB and ARGs was also investigated at field-scale. Two independent wastewater treatment plants both substantially reduced total ARG relative and absolute abundance through biological treatment and settling according to metagenomic analysis. The subsequent water reuse treatment train of one system produced water for non- potable purposes and found further reduction in ARGs after chlorination, but a five hundred percent increase in the relative abundance of ARGs in the subsequent distribution system. In the second plant, which employed a membrane-free ozone-biologically-activated carbon-granular activated carbon treatment train for indirect potable reuse, there were notable increases in total ARG relative abundance following ozonation and chlorination. However, these numbers attenuated below background aquifer levels before recharge. Culture-based analysis of these systems targeting resistant ESKAPE pathogens (Escherichia coil, Staphylococcus aureus, Klebsiella spp., Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterococcus spp.) indicated similar trends as the metagenomic ARG analysis for both systems, but was challenged by sub-optimal media for wastewater samples and low confirmation rates, limiting statistical analysis. In order to advance the application of NGS, molecular, and associated bioinformatic tools for monitoring pathogens and antibiotic resistance in environmental systems, newly emerging methods and field standards for antibiotic resistance assessment were also evaluated. Hybrid assembly, the assembly for both short and long metagenomic sequencing reads, were assessed with an in silico framework in order to determine which available assemblers produced the most accurate and long contigs. Hybrid assembly was found to produce longer and more accurate assemblies at all coverages by reducing error as compared to short read assembly, though the outputs differed in composition from long read assembly. Where it is possible, it is beneficial to sequence using both long- and short-read NGS technologies and employ hybrid assembly, but further validation is recommended. Genome resolved metagenomics has also emerged as a strategy to recover individual bacterial genomes from the mixed metagenomic samples though this is often not well validated. In order to address this, genomes were assembled from reclaimed water systems and were compared against whole-genome sequences of antibiotic resistant E.coli isolates. Metagenome-derived genomes were found to produce similar profiles in wastewater treatment plant influents. A final theme to this dissertation addresses the need to standardize targets, methodologies, and reporting of antibiotic resistance in the environment. A systematic literature review was conducted on assays for the enumeration of key ARGs across aquatic environments and recommendations are summarized for the production of comparable data. In sum, this dissertation advances knowledge about the occurrence of pathogens, ARB, and ARGs across aquatic and agricultural systems and across several countries. Advances are made in the application of NGS tools for environmental monitoring of antibiotic resistance and other targets and a path forward is recommended for continued improvement as both DNA sequencing technologies and computational methodologies continue to rapidly advance. / Doctor of Philosophy / Understanding bacteria in our engineered systems is critical to ensuring drinking water, recycled water, and manure-derived soil amendments are safe for downstream applications. As novel approaches for assessing bacteria are developed, standardized methods and evaluations much be developed to ensure that sound conclusions are made that can appropriately inform policy and practice for the protection of public health. This dissertation focuses on combining bacterial culture and DNA sequencing methods for the study of pathogens (i.e., disease-causing organisms) and antibiotic resistance (i.e., ability of some bacteria to survive antibiotic treatments) in agricultural manure management, water reuse, and drinking water systems. Additionally, this work sought to advance emergent metagenomic analysis tools, which provides a new and potentially powerful pathogen and antibiotic resistance monitoring approach through direct extraction and sequencing of DNA from environmental samples. Antibiotic resistance is a global health challenge and it has been widely recognized that wastewater and agriculture are key control points. When antibiotics are ingested by people or livestock, they select for resistant bacteria in the gut. Mitigation efforts are needed, particularly at wastewater treatment plants and on farms, to ensure that excreted antibiotics and resistant bacteria do not further propagate and pose a risk. However, additional challenges such as climate change have spurred the need for more efficient use of our water and nutrient resources. In this work I examined how nutrient and water reuse treatment methods affect antibiotic resistant bacteria and antibiotic resistance genes using DNA sequencing as well as culture-based methods. In order to assess agricultural practices, a systems approach was conducted at the greenhouse scale to identify key control points to stem the spread of antibiotic resistance when vegetables are grown in soils amended with cattle-derived manure fertilizers. Along the food production chain, vegetables (i.e., radish and lettuce) were found to harbor higher proportions of bacteria carrying antibiotic resistance genes, although the estimated numbers of these bacteria were lower. Solids from an international transect of wastewater treatment plants (Sweden, Switzerland, USA, India, Hong Kong, Phillippenes) were examined because they are also foten used as soil amendments. DNA sequencing of these solids revealed that total measured antibiotic resistance genes did not vary between treatment or continent of origin. Calculations were made to determine the range of total hypothetical outputs of ARGs if the biosolids are land applied. Wastewater reuse systems were also examined using culture and metagenomic DNA analysis so that living pathogens could be compared alongside the total (dead and alive) antibiotic resistance genes. While standard wastewater and subsequent water reuse treatments were found to reduce the absolute numbers of antibiotic resistance genes and bacteria in a treatment plant producing water for non-potable reuse (i.e., irrigation), increases in culturable resistant pathogens and antibiotic resistance genes were apparent in the distribution system (i.e., in the pipes conveying treated water to the point of use). Similar reductions in antibiotic resistant bacteria and resistance genes were also seen in a plant using more advanced treatment (ozonation paired with biofiltration) to produce water suitable for indirect potable reuse via aquifer recharge, but there were indications that ozone and chlorine can increase the proportion of antibiotic resistant bacteria. Finally, genomes were recovered from the metagenomic sequencing analysis and were compared to sequenced culture isolates to validate the capabilities of metagenomic analysis to re-assemble genomes at the strain level, which is often required for pathogen confirmation. Pathogens were also assessed in disrupted drinking water systems in Puerto Rico after Hurricane Maria. Small scale systems that were disrupted by the storm were sampled to identify if pathogens were measurable six months after the hurricane. This work revealed that genes attributed to pathogenic Leptospira were detected in all surface water reliant systems while Salmonella spp. were detected by culture and DNA methods, but only in the source surface and groundwaters, not in the distribution systems delivering water to from the treatment site to the tap. This research also contributed to the advancement of big data analysis pipelines as well as to the standardization of methods to ensure that data produced across studies are comparable. Hybrid assembly, an emergent method that combines both short and long metagenomic DNA sequences generated by different technologies to more accurately recover genomes, was found to improve reliability and accuracy of algorithms aimed at reassembling DNA fragments. Antibiotic resistance is a global challenge, but without standardized methodologies for environmental monitoring, it will be difficult to compare measurements across countries and treatment processes in order to identify effective mitigation strategies. A critical literature review was conducted on assays for the enumeration of key antibiotic resistance genes across aquatic environments so that comparable data can be generated. This will be critical to tap into the tremendous volumes of antibiotic resistance monitoring data being generated around the globe to help identify trends and inform solutions. Collectively, this dissertation advances knowledge about the occurrence of pathogens, antibiotic resistant bacteria and antibiotic resistance genes across aquatic and agricultural systems while also critically evaluating emerging methods for the detection of antibiotic resistance in the environment.

Memory corruption continues to plague modern software systems, as it has for decades. With the emergence of code-reuse attacks which take advantage of these vulnerabilities like Return- Oriented Programming (ROP) or non-control data attacks like Data-Oriented programming (DOP), defenses against these are growing thin. These attacks, and more advanced variations of them, are becoming more difficult to detect and to mitigate. In this arms race, it is critical to not only develop mitigation techniques, but also ways we can effectively deploy those techniques. In this work, we present rave - a framework which takes common design features of defenses against memory corruption and code-reuse and puts them in a real-world setting. Rave consists of two components: librave, the library responsible for static binary analysis and instrumentation, and CRIU-rave, an extended version of the battle-tested process migration tool available for Linux. In our prototype of this framework, we have shown that these tools can be used to rewrite live applications, like NGINX, with enough randomization to disrupt memory corruption attacks. This work is supported in part by ONR under grant N00014-18-1-2022 and NAVSEA/NEEC/NSWC Dahlgren under grant N00174-20-1-0009. / Master of Science / Memory corruption attacks continue to be a concrete threat against modern computer systems. Malicious actors can take advantage of related vulnerabilities to carry out more advance, hard-to-detect attacks which give them control of the target or leak critical information. Many works have been developed to defend against these sophisticated attacks and their triggers (memory corruption), but many struggle to be adopted into the real-world for reasons such as instability or difficulty in deployment. In this work, we introduce rave, a framework which seeks to address issues of stability and deployment by designing a way for defenders to coordinate and apply mitigation techniques in a real-world setting.

This research models the effects of software reuse on object-oriented software development, in particular, the reuse of C++ classes. Two types of reuse (with and without modification) are compared. The common traits of programmers who tend to reuse are identified, and some object-oriented software metrics are correlated with the inherent reusability of a C++ class. These issues are important because software reuse has been shown to increase productivity within the software development process. This research effort describes three experiments. The first characterizes the effects of reusing C++ classes on object-oriented software development using nine development process indicators. The second experiment uses ten similar process indicators to differentiate the effects of writing C++ classes from scratch versus reusing them without modification versus inheriting new classes from existing ones. The last experiment correlates some object-oriented metrics with the expert opinions of the reusability of C++ classes. This research has shown that the black box reuse (reuse without modification) of C++ classes is beneficial to object-oriented software development in many ways. Development time is reduced and system reliability increases. For abstract data type C++ classes, a set of fifteen skills and experiences are shown to be prominent in frequent class reusers. Lastly, a set of object-oriented metrics is used to predict C++ class reusability. All of these results can be used to increase programmer productivity when developing C++ software systems. / Ph. D.

How do we begin to deal with urbanism in the 21st Century? We are no longer working with the tabula rasa that we were two-hundred years ago; we are dealing with leftover infrastructure. Perhaps we should alter our mindset from "creating" to "RE-creating." We must accept the fact that cities have already been developed, they have already blossomed and many of them are now in late stages of decay. We must work with what is there now. In the 19th Century, builders and politicians believed that in order to reform a culture, they must rebuild. However, unlike our ancestors, we can no longer build without thinking about what the construction's future consequences will be. Environmental concerns are one of the major factors in today's society regarding the idea of "proper urban form." At the end of the industrial boom, many cities and urban centers have slowly started to become ghost towns of the industries that used to keep them alive. With fewer factory jobs, many families have moved outside of the city -- they have become heavily reliant on vehicular transportation to and from the vast parking lots in front of their "big box" office buildings and shopping centers. Consumerism has also contributed to suburban sprawl which is quickly hastening our climate's deterioration. We are rapidly using up our natural resources. In many instances, we are degrading the soil, deforesting our landscape, and destroying important eco-systems, like rainforests and glacial formations. We are using them up faster than they can repair themselves. Because our environment is NOT an unlimited resource, we need to begin to be more proactive about the way we let people treat our home. We must find ways to reduce the effects of what we do and what we have already done. We must create a means of reducing our footprint on the earth. We must find proper ways to dispose of our waste. We must stop sprawling outward, when there are plenty of well-built structures that we can begin to adapt, renovate and re-use. This project examines an instance in Lynchburg, Virginia -- wherein a turn-of the century produce-warehouse has outlived its purpose and now faces a turning point. I propose that we make use of its sturdy walls, floors and interesting character and give it a 21st Century purpose. / Master of Architecture