VictorJuiz/thesis huggingface dataset:
Design process communication methodology [electronic resource]

Building project design teams struggle to (1) collaborate around processes within projects, (2) share processes between projects, and (3) understand opportunities for investment in improving processes across projects. Overcoming each challenge requires effective and efficient communication of design processes. Yet, methods for communicating design processes from the design process communication research field are too cumbersome to be useful during design, and methods from the project information management research field focus only on information exchange and not process communication. To address these limitations, I aggregate findings from organizational science, human computer interaction, and process modeling fields to develop the characteristics of the Design Process Communication Methodology (DPCM). DPCM is Computable, Embedded, Modular, Personalized, Scalable, Shared, Social, and Transparent. Enabling these characteristics, DPCM consists of elements which represent and contextualize processes and methods that enable designers to capture and retrieve processes. To test DPCM, I map the elements and method s to the Process Integration Platform (PIP). PIP is a web tool that enables project teams to organize and share files as nodes in an information dependency map that emerges as the team works. Results from the use of PIP in student design charrettes and class projects provide evidence for the power of DPCM to effectively and efficiently communicate building design processes within project teams, between project teams, and across project teams. I claim DPCM as a contribution to the fields of design process management and project information management. DPCM lays the foundation for commercial software that shifts focus away from incremental and fragmented process improvement toward a platform that nurtures emergence of (1) improved multi-disciplinary collaboration, (2) process knowledge sharing, and (3) innovation-enabling understanding of existing processes.

Advisor: Fischer Martin
Haymaker John primary advisor. Thesis advisor
Winograd Terry advisor. Thesis advisor
Design scenarios methodology - enabling requirements-driven design spaces [electronic resource]

During the conceptual design process, the building shape, orientation, materials and other major properties are established, all of which have a substantial impact on multi-aspect performance. In this process, multidisciplinary teams define project objectives, create various alternatives, and try to understand their impacts and value. With non-parametric Computer Aided Design (CAD) methods designers produce and analyze as few as three alternatives, whereas with parametric CAD -- they can generate thousands. However, with current parametric methods, CAD experts lack a comprehensive method to build and analyze multi-objective parametric models. Therefore the resulting models do not effectively encapsulate multi-objective value measures. This research introduces the Design Scenarios Methodology (DS), which builds on research from Systems Engineering, Process Modeling, and Parametric Modeling. With DS, Enablers use Methods to create Elements using five interconnected models to define (1) project stakeholders and their objectives, (2) designer logic used to address objectives, (3) the connection between designer logic and computable models to generate alternatives, (4) the predicted impact and (5) value of the generated alternatives. I implemented DS as a web-based software prototype and tested it on an industry project. The results provide evidence that the DS method provides CAD experts with well-defined logic and parameters for addressing objectives and the process enables creating parametric alternatives with clear multi-objective values that potentially provide clients with better building designs. This thesis lays the foundation for future research on automating the design alternative generation and analyses processes by leveraging such well established methods as Multi-Disciplinary Optimization.

Advisor: Fischer Martin
Haymaker John primary advisor. Thesis advisor
Bazjanac Vladimir advisor. Thesis advisor
Cutkosky Mark R. advisor. Thesis advisor
Design, synthesis, and evaluation of molecular transporters for probe, drug, and siRNA delivery [electronic resource]

My graduate studies have focused on the design, synthesis, and biological evaluation of novel probe and drug delivery technologies. This research has explored the development of new molecular transporter scaffolds with a focus on step economy and translational costs as well as evaluation of their uptake and delivery properties in cells and animals. Chapter 1 provides a historical context and overview of guanidinium-rich molecular transporter technology. Chapter 2 describes the development of a new family of guanidinium-rich oligocarbonate molecular transporter which are flexibly and efficiently assembled by a one-step oligomerization strategy. These novel oligocarbonate transporters were shown to exhibit excellent uptake properties both in cells and animal models. Chapter 3 is directed at the utility of an oligomerization approach to generate molecular transporters by the design, synthesis, and evaluation of new aphipathic co-oligomers for the delivery of siRNA, an oligonucleotide cargo of intense therapeutic interest. Amphipathic carbonate co-oligomers were prepared by an oligomerization strategy and demonstrated to effectively package, deliver, and release functional siRNA in cells. Chapter 4 describes the effects of a branched guanidinium array on the transport and delivery efficiency of releasable dendrimeric guanidinium-rich transporters. These transporters were synthesized and demonstrated to deliver and release a small molecule for turnover by its intracellular target enzyme by bioluminescence assays in cells and transgenic animal models. Chapter 5 describes the design, synthesis, and preliminary biological evaluation of lipidated molecular transporter derivatives of the immunosuppressant drug rapamycin for topical delivery.

Keywords: Chemistry
Advisor: Wender Paul A. primary advisor. Thesis advisor
Du Bois Justin advisor. Thesis advisor
Kool Eric T. advisor. Thesis advisor
The design, synthesis, and evaluation of simplified, function-oriented analogs of the daphnane diterpene orthoesters and the laulimalides [electronic resource]

In this work, a function-oriented array of simplified analogs of the daphnane diterpene orthoester class of natural products bearing palmitate, phenyl, or phenylacetyl orthoesters was synthesized starting from commerically available starting materials via a key late stage common diversification intermediate. These families of novel compounds were evaluated for both selective PKC activation and growth inhibition of K562 (myleogenous leukemia) cancer cells. While these analogs showed no growth inhibitory activity in K562 cells up to concentrations of 10 micromolar, they did display varying profiles of PKC activation. One analog in particular demonstrated the ability to activate and cause translocation of conventional PKC b1 and novel PKC d to the same extent as resiniferonol, a potent natural resiniferonoid. A second analog, however, was found to activate novel PKC d selectively over conventional PKC b1; surprisingly, resiniferonol did not share this selectivity profile. Because the simplified, functional analogs synthesized in this study were shown to activate PKC while having no growth inhibitory activity, these compounds should be further investigated for their potential as therapeutic leads for the treatment of diseases like Alzheimer's or Parkinson's, in which (selective) activation of PKC could serve a therapeutic purpose without being plagued by growth inhibitory pathways.

Keywords: Chemistry
Advisor: Wender Paul A. primary advisor. Thesis advisor
Du Bois Justin advisor. Thesis advisor
Kanan Matthew William
Designers as brokers [electronic resource] : the development of field trip programs at three informal science institutions

Field trips represent potentially powerful bridges between formal and informal science education. This study investigates the work of designing and developing school field trip programs at informal science institutions (ISIs). Using a model of innovation through "knowledge brokering" (Hargadon, 2002), comparative case studies were conducted at three California ISIs: Monterey Bay Aquarium, California Academy of Sciences, and Marine Science Institute. Knowledge brokering describes a process of learning about existing resources in disparate social domains and recombining these resources into innovative solutions. At each ISI, the work of one field trip program designer was investigated through interviews, resource mapping exercises, materials gathering, and observations. Across cases, program designers used knowledge of science content, objects, learning theories, institutional context, and their audience's needs and motivations. Working in their different institutional contexts, designers experienced different opportunities, supports, and challenges around knowledge brokering. Knowledge brokering occurred to the greatest extent in the case of the Aquarium designer; the Academy designer encountered some obstacles, many of which were related to a major institutional transition; and the Institute designer, working at a small institution with comparably fewer resources, had limited opportunities to broker knowledge from disparate domains of expertise. Although it was a useful conceptual lens, issues related to thresholds for evidence and multiple levels of analysis presented challenges in applying the knowledge brokering model to the realm of field trip design. This research urges study of how to support the work of informal science educators who, in designing these programs, shape the type and quality of experiences that are possible for learners.

Keywords: Education.
Advisor: Shavelson Richard J.
Ardoin Nicole M. (Nicole Michele) advisor. Thesis advisor
Osborne Jonathan advisor. Thesis advisor
Determination of human articular cartilage condition using magnetic resonance imaging, creep indentation testing and biochemistry [electronic resource]

Human articular cartilage can degrade, losing functional quality and eventually exposing bone surfaces; when significantly advanced, this cartilage degradation can be diagnosed as osteoarthritis (OA). Currently, knee OA can be diagnosed only when the disease is advanced and the patient is suffering from pain. There is no cure for knee OA, nor are there prevent preventative therapies; current treatment strategies relieve the pain of OA or completely replace the knee joint. To evaluate potential therapies and treatments, we need a method that can identify and measure changes to cartilage prior to the onset of degradation. Magnetic resonance imaging (MRI) is a potentially powerful tool to non-invasively evaluate the progression of knee OA by mapping MR image parameters to molecular and material properties that are known to change with disease. The goal of this dissertation was to determine MR image parameters that can be used to evaluate the progression of OA. We examined the biphasic and viscoelastic models of cartilage to determine cartilage material properties from indentation creep tests. We compared initial elastic modulus and cartilage macromolecules to MRI parameters, specifically T2 and T1rho relaxation times and T1rho dispersion. We determined that a predictive model based on T1rho relaxation time maps, which accounts for T2 relaxation time and the effects of age, may estimate longitudinal trends in GAG content in the same person. In addition, a simple T1rho dispersion estimate has the potential for substantial clinical impact by measuring changes in cartilage initial elastic modulus and macromolecules non-invasively. This work is an important step toward developing clinical methods for evaluating cartilage functional condition, and in turn, to advance work towards preventing and treating knee OA.

Keywords: Mechanical Engineering
Advisor: Delp Scott primary advisor. Thesis advisor
Gold Garry E.
Beaupré Gary Scott advisor. Thesis advisor
Determining the Folded and Unfolded Structure of the HIV TAR RNA Using Small-Angle X-ray Scattering

In biological macromolecules, such as proteins or RNA, structure determines function. While most RNA primary sequences code for proteins, some RNA, called non-coding RNA, fold into a range of tertiary structures to regulate transcription of the coding RNA. These tertiary structures can be influenced by several environmental factors, including counterion concentrations and ligands that bind to specific sites on the RNA and induce folding. Thus knowledge of the dynamic range of an RNA molecule in solution is crucial to understanding its function in vivo. In this experiment, the structure and folding landscape of the transactivation response element (TAR) RNA from the human immunodeficiency virus (HIV) was probed using small-angle x-ray scattering (SAXS) techniques. TAR takes the form of a common structural motif in RNA folding, so its conformational properties are relevant to the understanding of most structured RNAs. Moreover, the TAR RNA plays a crucial role in the lifecycle of HIV; knowledge about its structure will inform studies of its function and could contribute to the search for an HIV drug. In the first SAXS measurement of HIV TAR, we probed the structure of the TAR RNA in its unfolded state, as well as in several different ligand and counterion-induced folded conformations.

Keywords: Physics
Das, Rhiju
transactivation response element
TAR RNA
small-angle x-ray scattering
SAXS
Thesis
Developing Aiptasia pallida as a tractable model system for cnidarian-dinoflagellate symbiosis [electronic resource] : identifying transferred metabolites and designing tools for analysis of ultra-high-throughput-sequencing data

This dissertation describes a general method for identifying and roughly quantifying the metabolites that are produced by symbiotic dinoflagellates and transferred to cnidarian hosts. I developed a system of rapid filtration and gas chromatography-mass spectrometry (GC-MS) to identify these compounds in the anemone tissue and dinoflagellates separately. I used 13C-sodium bicarbonate to label compounds produced from newly-fixed carbon; the principal compound detected in the animal was glucose. I developed a way to visualize these and other large GC-MS datasets using open-source software. I also built tools for analyzing Ultra-High-Throughput-Sequencing (UHTS) data, and these were useful in the de novo assembly of the Aiptasia pallida transcriptome. One tool I developed compares each read to each other read using a MapReduce framework to merge near-duplicate reads and reduce redundancy in the dataset. In addition, our lab sequenced symbiotic animals and therefore often worked with pools of sequences from multiple organisms. I developed a tool for identifying which transcript sequence was produced by which organism in a symbiotic ecosystem: it was 99% accurate on high-quality validation data.

Keywords: Genetics
Advisor: Pringle John
Altman Russ advisor. Thesis advisor
Long Sharon R. advisor. Thesis advisor
Sherlock Gavin advisor. Thesis advisor
Development and testing of computational models of a flapping wing and a high altitude long endurance aircraft for high-fidelity nonlinear multidisciplinary simulations [electronic resource]

In the present thesis numerical aeroelastic models are developed for a Flapping Wing System and a High Altitude Long Endurance Aircraft. Fluid and structural models are created separately. Conception and development of highly complex and detailed models for both systems are explained. Common to both models is the characteristic large displacements of their structural dynamic behavior. This raises the need for nonlinear considerations on the structural solver. For the fluid solver the Arbitrary Lagrangian Eulerian formulation revealed to be not appropriate due to the lack of robustness under large deformations of the mesh. Hence, an Eulerian framework is used which showed to be successful in simulating the aeroelastic response of the systems. Numerical tests conducted separately on the fluid and structural models of each system are presented. These are done to study their character and check if their behavior seems physical since no corresponding experimental data is available. After successful tests, an aeroelastic simulation is performed for both systems, demonstrating the readability of the models for fluid-structure interaction analyses. Since the considered models tend to be large-scale, they require massive computational effort to be solved. Finally, a study on Reduced Order Modeling of an aeroelastic problem is performed; this as an attempt to find a way of reducing the resources required to analyze the contemplated systems.

Keywords: Aeronautics and Astronautics
Advisor: Farhat Charbel advisor. Thesis advisor
Development Assistance for Health as a Weapon Against Threats of Infectious Diseases: Evidence from aid for HIV and Tuberculosis

Prior research on allocation of development assistance (DAH) for health has focused primarily on recipient need, and not on provider interest. Provider interests, in the form of financial or welfare benefits, can influence donor behavior by affecting prioritization of goals or modifying aid amounts. Shiffman (2006) proposes that funding for HIV and tuberculosis have risen disproportionately because of their burden on industrialized countries, while funding for malaria – a tropical disease – has remained relatively low. Of many possible forms of provider interest, this paper focuses on the incentives of the donor states to protect the public health of its own residents by allocating DAH to the control of infectious diseases abroad. If this incentive does exist, I expect the DAH amount for a disease to increase with the domestic prevalence of the disease in the donor country. I use a multiple regression strategy to estimate the effect that prevalence has on DAH allocated per year to HIV and tuberculosis from 1990 to 2009. My analysis provides evidence that HIV and TB prevalence in donor country positively affects international health aid granted for those diseases.

Keywords:  Department of Economics
Stanford Department of Economics
provider interest
aid allocation
development assistance for health
public health
Thesis
Advisor: Bhattacharya Jayanta
Development of a diode laser sensor for measurement of mass flux in supersonic flow [electronic resource]

Mass flux is one of the most critical parameters in the calculation of engine thrust and assessment of aeroengine performance. Conventional mass-flux measurements are facilitated with invasive temperature and pressure probes which tend to disturb the flow, generate shock structures, have limited lifetimes, and require frequent maintenance. In response, there is a growing opportunity for tunable diode laser (TDL) diagnostics, which can be deployed noninvasively with fast time response and high accuracy. The focus of this work is the development of a TDL mass-flux sensor based on water vapor absorption for deployment in a combustion-driven Mach 2.7 wind tunnel at NASA Langley. The 1f-normalized wavelength-modulation spectroscopy with second harmonic detection (WMS-2f/1f) technique was employed for its unique noise-rejection capability and increase in signal-to-noise ratio; this method was used to measure velocity with improved precision while simultaneously determining temperature. Density was inferred from an independent pressure measurement and the ideal gas law. The sensor temperature measurements were validated against thermocouple readings in a heated cell at Stanford to within 1%. Measurements of velocity were made in a low-speed wind tunnel with accuracy within 0.5m/s of a pitot probe reading; a reduction of 50% in the standard deviation of the velocity measurement was also observed by using optimized WMS-2f/1f. In addition, the influence of flow nonuniformity on line-of-sight (LOS) measurements is investigated by simulating path-integrated lineshapes from computational fluid dynamics (CFD) solutions. The results are quantified in order to develop a correction to the path-integrated measurements obtained in this work. The capstone mass-flux measurements were performed in the NASA Langley Direct-Connect Supersonic Combustion Test Facility isolator. Temporally resolved velocity data was corrected according to the nonuniformity analysis of path-integrated lineshapes, bringing the sensor velocity measurement within 0.25% of the value predicted by the facility code (4m/s in a 1630m/s flow). Temperature measurements were made with high precision (10K standard deviation in a 990K flow), and agreement with the predicted value was also within 1%. Mass-flux measurements had similar precision (standard deviation less than 1% of full scale) and accuracy (within 1% of predicted value). Finally, spatially resolved velocity and mass-flux data taken along both the height and width of the isolator were found to be in close agreement with the CFD solution. These results show that TDL mass-flux sensing based on WMS-2f/1f can produce temporally and spatially resolved measurements with high precision and accuracy in a supersonic flow, thus demonstrating the sensor's potential for future deployment in unknown mass-capture environments such as inlet models and flight tests.

Keywords: Mechanical Engineering
Advisor: Hanson Ronald primary advisor. Thesis advisor
Cantwell Brian advisor. Thesis advisor
Mungal Mark Godfrey advisor. Thesis advisor
Development of a novel method to purify and culture mature rat astrocytes [electronic resource]

Astrocytes constitute more than half of the human brain, yet their functions have yet to be fully elucidated largely due to a lack of a good and pure in vitro culture system. The inability to purify and culture brain astrocytes has long hindered studies of their function. Although astrocyte progenitor cells can be cultured from neonatal brain, culture of more differentiated mature astrocytes from postnatal brain has not previously been possible. Here I report a new method for the prospective purification of astrocytes by immunopanning (IP-astrocytes) and have used this method to investigate several fundamental properties, functions of astrocytes and neuron-glial interactions. I show that these highly purified astrocytes, like neurons, undergo apoptosis in culture, but that vascular cells as well as exogenous HBEGF and Wnt7a strongly promote their survival in serum-free culture. Similarly, I found that developing astrocytes in vivo undergo apoptosis and that the vast majority of surviving astrocytes in vivo contact blood vessels and hypothesise that developing astrocytes may normally be matched to blood vessels by competing for a limited supply of vascular trophic factors. In contrast to the more traditional neonatal astrocyte cultures prepared via a method developed by McCarthy and de Vellis (1980) (MD-astrocytes), the gene profiles and functions of the purified postnatal astrocytes in serum-free culture much more closely resembled that of astrocytes in vivo. These astrocytes also strongly promoted synapse formation and function. I have also identified genes that are induced by serum and show that serum exposure to astrocytes causes massive and irreversible changes of gene expression as well as astrocyte function. In addition, I have highlighted several features of MD-astrocytes that are different from IP-astrocytes. Together, the data suggests that I have developed a culture system that is more representative of the in vivo state. This culture system will be of interest to a broad range of neuroscientists as it provides a simplified and tractable system to study the functions and properties of astrocytes both in the normal and diseased states.

Advisor: Barres Ben
McConnell Susan K. advisor. Thesis advisor
Shen Kang
Talbot William