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Online 1. A scalable and interoperable cyberinfrastructure platform for civil infrastructure monitoring [2019]

Description
Book — 1 online resource.
Summary
Civil infrastructure monitoring is an important technology that provides accurate and objective data on the health condition of a structure by leveraging sensor technologies. Together with routine maintenance and inspection, civil infrastructure monitoring enables the diagnosis of potential structural problems and the prognosis for the need of structural strengthening and repairs. As sensor technologies mature and become economically affordable, their deployment for civil infrastructure monitoring will continue to grow to collect more detailed data about the structures. The data collected from civil infrastructure monitoring systems offers promising opportunities to find meaningful information, knowledge and insight that can improve decision making processes. Furthermore, advances in sensing and communication technologies will eventually realize the concept of cyber-physical systems (CPS) that tightly integrate physical systems and cyber systems to monitor, analyze, coordinate and control the operations of physical systems. Nevertheless, the increasing use of sensors will also lead to significant data management issues. Civil infrastructure monitoring systems instrumented with dense sensor networks will be inundated with unprecedented volume and diverse types of data that need to be processed, interpreted and brought forth to support system operations. The utilization of such "big data" will be significantly limited unless a proper data management platform, which can efficiently store, manage, retrieve, share, interface, link and integrate data, is developed. This thesis describes a cyberinfrastructure platform for civil infrastructure monitoring with an emphasis on system scalability and interoperability. The cyberinfrastructure platform brings together information and communication technologies (ICT), including information modeling, NoSQL database, cloud computing and web services, for effective data management. An information modeling framework with application to bridge monitoring is designed to facilitate data interoperability and data integration. A NoSQL-based data management system is developed to enable scalable, flexible and fault-tolerant management of monitoring data. Cloud computing is adopted as a scalable, reliable and accessible computing infrastructure. Platform-neutral web services are developed to enable easy access to the cloud resources and data involved in engineering systems via standard communication protocols. For demonstration, the cyberinfrastructure platform is implemented for the monitoring of bridges along the I-275 corridor in the State of Michigan. The results show that the cyberinfrastructure platform can effectively manage the sensor data and domain-specific information and facilitate data sharing, integration and utilization.
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Online 2. Analysis, evaluation, and improvement of performance-based earthquake engineering damage and loss predictions [2019]

Description
Book — 1 online resource.
Summary
Performance-based earthquake engineering (PBEE) has in many ways revolutionized the thinking about seismic engineering design and acceptable performance of buildings in earthquakes. It is now making its way into commercial engineering design and risk analysis practice, as engineers aim to design better-performing buildings, and holders of mortgage or insurance instruments try to better understand the risk they face from damage to associated buildings. Some parts of the calculations (e.g. structural response) have been extensively assessed and validated. There are few similar studies, however, that focus on the damage and loss predictions. The purpose of this dissertation is to address this, by analyzing, evaluating, and improving the damage and loss predictions. The specific PBEE methodology examined in this dissertation is the FEMA P-58 Seismic Performance Assessment Procedure. FEMA P-58 damage and loss predictions are analyzed, to determine how they are impacted by other parts of the calculations. Firstly, variance-based sensitivity analyses are conducted to investigate the interaction of loss predictions with different inputs to the calculations. Of the six inputs considered in the analyses, it is found that predictions of building repair cost (as a fraction of replacement value) are most sensitive to shaking intensity and building age, while building re-occupancy time predictions are most sensitive to shaking intensity and building lateral system. Secondly, a methodology is developed to quantify the impact of available structural response data from seismic instrumentation on the quality of the damage and loss predictions. The density of instrumentation examined using the methodology ranges from the case in which all floors are instrumented to that in which no floors are instrumented and simplified procedures are used to produce structural response predictions. It is found that the quality of the predictions generally improves as the density of seismic instrumentation increases, but it is not crucial for the density to be very high to achieve reasonable accuracy in both damage and loss predictions (although this may depend on the arrangement of instrumentation within a building). Loss predictions are evaluated using data observed in previous seismic events, to understand the degree to which they reflect real-life consequences of earthquakes. A methodology is developed for evaluating the ability of FEMA P-58 component-level losses to predict damage observed for groups of buildings. It is found in applications of the methodology that FEMA P-58 non-structural component-level loss predictions provide more insight into damage than variations in ground shaking between buildings. Finally, this dissertation includes a number of recommendations for improving non-structural mechanical component fragility functions and associated loss predictions used in FEMA-58 calculations. The fitting technique currently used for the functions does not converge in some cases, and the methodology used to predict anchored mechanical component losses can lead to some unexpected results, such as non-smooth variation of repair costs with anchorage capacity. An alternative statistical technique is proposed for fitting the fragility functions that mitigates the non-convergence problems when fitting and makes predictions that better align with damage observed in past events. A more intuitive methodology for predicting anchored mechanical component losses is also suggested. The findings of this dissertation help to enhance understanding of, and improve, the damage and loss predictions used in the FEMA P-58 seismic performance assessment procedure. They ultimately enable various stakeholders, such as building owners, design professionals, lenders, and insurers, to make more informed decisions about seismic risk.
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Online 3. Applications of atomic layer deposition for next-generation nanoscale devices [2019]

Description
Book — 1 online resource.
Summary
Atomic Layer Deposition (ALD) is a thin film deposition technique that has gained prominence in recent years due to its ability to synthesize highly conformal and uniform films, with precise thickness control and for a wide range of materials. This work explores how the unique properties of ALD films can be leveraged through novel nanofabrication processes to enable higher performance devices. First, a comprehensive characterization of the etch rates of 9 oxide ALD films in 20 wet chemicals and vapor etchants is presented, as knowing the films' etch rates and their compatibility with commonly used processing chemicals is crucially important when integrating them into nanofabrication processes. Second, a new process is described that, by taking advantage of ALD films' excellent properties as etch stop layers for vapor releases, allows the simultaneous release of suspended structures of varying sizes and arbitrary shapes with high accuracy. This so-called "sandbox" process can be incorporated into the fabrication of many kinds of devices, and has been successfully employed for aluminum nitride piezoelectric resonators, resulting in a record high figure of merit. Finally, the development of thermal accelerometers featuring ultrathin suspended platinum thermistors with thicknesses down to 8 nm is presented. Using plasma-enhanced ALD of platinum for the first time in a thermal accelerometer enables a 100x reduction in beam cross-section compared to previous work. Plasma treatments and nucleation layer dependencies of ALD platinum are investigated to further enhance material properties. Novel fabrication processes allow large cavity sizes of up to 500 μm depth and 4000 μm length, resulting in unprecedentedly high aspect ratios exceeding 100,000:1, which confer many benefits such as increased heating efficiency and decreased thermal time constants.
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Online 4. Assessment of physical function from patterns in routine physical activity measured by wearable activity monitors [2019]

  • Agarwal, Vibhu, author.
  • [Stanford, California] : [Stanford University], 2019.
Description
Book — 1 online resource.
Summary
Limitations in physical functioning can lead to dire health and financial consequences. However, the progression of physical function impairment interacts with many different factors, such as organ function, activities and the environment. It is suspected that the complexity of physical function evaluation methods contributes to the low prevalence of function assessments in routine care. Earlier studies have shown that a bidirectional and monotonic relationship exists between physical activity and function. Wearable activity monitors (WAM) -- devices equipped with one or more accelerometers, offer an opportunity to infer physical function from the observed physical activity objectively and at scale. However, efforts to infer function from such activity measurements have been limited. In this dissertation I present methods to infer physical function from daily activity data. Using free-living activity data from the physical activity studies in the Osteoarthritis Initiative, I show that activity measurements obtained by a WAM are sensitive to changes in physical function, if we use an appropriate representation for daily activity. Further, I show that a representation of physical activity that quantifies a subject's engagement in different classes of activity patterns, improves the performance in a physical function classification task. I also demonstrate how such an activity representation may be constructed in an unsupervised manner, obviating the need for time consuming annotation of activity data. Finally, I motivate the case for a composite score of physical function and present two methods for deriving such a score from free-living activity. I also present evaluations of the computed score on predicting key events in the natural history of knee osteoarthritis. Inferring physical function from wearable activity monitors will enable remote monitoring of function, which in turn will facilitate better delivery of care to patients, at a lower cost.
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Online 5. Association of Primary Care Physician Supply With Population Mortality in the United States, 2005-2015 [2019]

Description
Software/Multimedia
Summary
Importance Recent US health care reforms incentivize improved population health outcomes and primary care functions. It remains unclear how much improving primary care physician supply can improve population health, independent of other health care and socioeconomic factors. Objectives To identify primary care physician supply changes across US counties from 2005-2015 and associations between such changes and population mortality. Design, Setting, and Participants This epidemiological study evaluated US population data and individual-level claims data linked to mortality from 2005 to 2015 against changes in primary care and specialist physician supply from 2005 to 2015. Data from 3142 US counties, 7144 primary care service areas, and 306 hospital referral regions were used to investigate the association of primary care physician supply with changes in life expectancy and cause-specific mortality after adjustment for health care, demographic, socioeconomic, and behavioral covariates. Analysis was performed from March to July 2018. Main Outcomes and Measures Age-standardized life expectancy, cause-specific mortality, and restricted mean survival time. Results Primary care physician supply increased from 196 014 physicians in 2005 to 204 419 in 2015. Owing to disproportionate losses of primary care physicians in some counties and population increases, the mean (SD) density of primary care physicians relative to population size decreased from 46.6 per 100 000 population (95% CI, 0.0-114.6 per 100 000 population) to 41.4 per 100 000 population (95% CI, 0.0-108.6 per 100 000 population), with greater losses in rural areas. In adjusted mixed-effects regressions, every 10 additional primary care physicians per 100 000 population was associated with a 51.5-day increase in life expectancy (95% CI, 29.5-73.5 days; 0.2% increase), whereas an increase in 10 specialist physicians per 100 000 population corresponded to a 19.2-day increase (95% CI, 7.0-31.3 days). A total of 10 additional primary care physicians per 100 000 population was associated with reduced cardiovascular, cancer, and respiratory mortality by 0.9% to 1.4%. Analyses at different geographic levels, using instrumental variable regressions, or at the individual level found similar benefits associated with primary care supply. Conclusions and Relevance Greater primary care physician supply was associated with lower mortality, but per capita supply decreased between 2005 and 2015. Programs to explicitly direct more resources to primary care physician supply may be important for population health.
Importance Recent US health care reforms incentivize improved population health outcomes and primary care functions. It remains unclear how much improving primary care physician supply can improve population health, independent of other health care and socioeconomic factors. Objectives To identify primary care physician supply changes across US counties from 2005-2015 and associations between such changes and population mortality. Design, Setting, and Participants This epidemiological study evaluated US population data and individual-level claims data linked to mortality from 2005 to 2015 against changes in primary care and specialist physician supply from 2005 to 2015. Data from 3142 US counties, 7144 primary care service areas, and 306 hospital referral regions were used to investigate the association of primary care physician supply with changes in life expectancy and cause-specific mortality after adjustment for health care, demographic, socioeconomic, and behavioral covariates. Analysis was performed from March to July 2018. Main Outcomes and Measures Age-standardized life expectancy, cause-specific mortality, and restricted mean survival time. Results Primary care physician supply increased from 196 014 physicians in 2005 to 204 419 in 2015. Owing to disproportionate losses of primary care physicians in some counties and population increases, the mean (SD) density of primary care physicians relative to population size decreased from 46.6 per 100 000 population (95% CI, 0.0-114.6 per 100 000 population) to 41.4 per 100 000 population (95% CI, 0.0-108.6 per 100 000 population), with greater losses in rural areas. In adjusted mixed-effects regressions, every 10 additional primary care physicians per 100 000 population was associated with a 51.5-day increase in life expectancy (95% CI, 29.5-73.5 days; 0.2% increase), whereas an increase in 10 specialist physicians per 100 000 population corresponded to a 19.2-day increase (95% CI, 7.0-31.3 days). A total of 10 additional primary care physicians per 100 000 population was associated with reduced cardiovascular, cancer, and respiratory mortality by 0.9% to 1.4%. Analyses at different geographic levels, using instrumental variable regressions, or at the individual level found similar benefits associated with primary care supply. Conclusions and Relevance Greater primary care physician supply was associated with lower mortality, but per capita supply decreased between 2005 and 2015. Programs to explicitly direct more resources to primary care physician supply may be important for population health.
Collection
Stanford Project for Open Knowledge in Epidemiology (SPOKE)

Online 6. The asymmetric synthesis of acyclic tetrasubstituted stereocenters by palladium-catalyzed allylic alkylation [2019]

Description
Book — 1 online resource.
Summary
Herein are described strategies for the asymmetric synthesis of acyclic tetrasubstituted stereocenters using palladium-catalyzed allylic alkylation. In particular prochiral nucleophiles are exploited for the synthesis of acyclic alpha tertiary hydroxyketones, fully substituted nitroalkanes, and all-carbon quaternary stereocenters. The problem of O-alkylation in benzylic nitronate synthesis was overcome by the use of a decarboxylative asymmetric allylic alkylation of allyl alpha nitroesters. Extensive screening of reaction conditions revealed a unique ligand and solvent combination that proved crucial for achieving high chemo- and enantioselectivity in this challenging reaction. Substrates were readily synthesized via a combinatorial cross-Claisen / alpha arylation protocol, and the method was highlighted by chemoselective functional group interconversions of a highly elaborated substrate. Boronic acids were exploited as templates of ene-diolate systems to solve a longstanding problem of direct asymmetric C-alkylation of alpha hydroxyketones. This process was rendered chemo-, regio-, and enantioselective in allylation reactions, while point and axial chirality were efficiently set in allylic alkylations of racemic allene substrates via a dynamic kinetic asymmetric transformation. This method represents one of the first examples where point and axial chirality are effectively set in allylic alkylation. As a follow-up to this work, enol boranes were found to be effective pronucleophiles in palladium-catalyzed allylic alkylation reactions. A 1,4-hydroboration reaction was exploited for the thermal generation of regio-defined enol boranes, and a unique electron-deficient ligand was found to exhibit differential reactivity in the subsequent alkylation reaction. This chemistry was further extended to provide a room temperature alkylation of ester derived enol boranes, in particular, unactivated esters. A preparative application was demonstrated in the synthesis of acyclic all-carbon quaternary stereocenters, where the stereoselectivity was a function of the identities of a chiral auxiliary, a chiral ligand, and a designer leaving group. It is hoped that this chemistry may spur broader interest in metal-catalyzed reactions of enol boranes.
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Online 7. Augmenting human driving via steering wheel skin stretch haptics [2019]

Description
Book — 1 online resource.
Summary
Cars are growing smarter as they incorporate improvements in sensing, computing and communication. They increasingly are able to monitor the environment, detect impending events, and make decisions, sometimes with higher speed and accuracy than is possible for the human driver. While this helps drivers in many ways, it also reduces situational awareness and driver ability to respond to emergencies, and it remains an open question how best to communicate this information. This thesis examines haptic skin stretch at the steering wheel as a way to improve communication from car to driver and augment driving ability. A steering wheel with an embedded skin stretch display was designed that is compact, lightweight, and allows holding at any position. Rotational motion of the front surface of the rim produces lateral deformation of the skin of the hands, stimulating slowly- and rapidly-adapting mechanoreceptors. The resulting haptic stimuli communicate magnitude, direction, and speed information. This thesis describes a series of experiments with this device characterizing the abilities of humans to perceive the feedback and react appropriately in various driving scenarios. In the first, human ability to perceive directional information in a driving vehicle in suburban traffic was assessed, with results generally consistent with those in stationary applications; however, a higher and especially faster rate of stretch application was preferred. In the second experiment, tests are conducted to determine whether drivers can correctly perceive and react to skin stretch navigation cues, which are compared to audio navigation cues during an auditory distraction task simulating a phone call. Results showed haptic feedback was at least as accurate as audio feedback and was less distracting. In the third experiment, human ability to utilize skin stretch for obstacle avoidance is examined: in particular, whether they could predict the size and location of obstacles. Subjects were found to perform correct maneuvers with high accuracy, modifying both maneuver direction and size based on the stimulus. Finally, an experiment in a different application, medical needle guidance, provided general insight in how best to provide steering information through skin deformation. Particular attention is given to the ability of skin stretch to alert the driver about impending events, inform about direction, and communicate the magnitude of an event. Results show that all three types of information can be conveyed, with attention to details of how skin stretch is imparted in terms of stimulus pattern, frequency, and magnitude.
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Online 8. Challenges in CT with photon counting detectors [2019]

Description
Book — 1 online resource.
Summary
With many attractive attributes including improved tissue characterization, reduced noise, and lower dose, photon counting detectors (PCDs) with multiple energy bins are being considered for clinical CT systems. A major problem with PCDs is the slow count rate, resulting in count rate loss and pulse pileup. Another challenge to PCDs with multiple energy bins is the large amount of projection data acquired that must be transferred in real time through slip rings to data storage subsystems, causing a bandwidth bottleneck problem. Our goal is to address these challenges with a dynamic bowtie filter, a pulse pileup modeling, and a compression algorithm for PCD projection data. A dynamic bowtie modulates flux distribution as a function of fan and view angles to reduce dose, scatter, and detector dynamic range. One approach, the piecewise-linear attenuator (Hsieh and Pelc, Med Phys 2013), consists of multiple wedges, each of which covers a different fan angle range and is moved in the axial direction to change the thickness seen in an axial slice. Our implementation of the filter with precision components and a control algorithm reduces the detected flux dynamic range to 42 for a chest and 25 for an abdomen, corresponding to a reduction factor of 5 and 11 from the object scans without the bowtie. The thickness profile of the piecewise-linear attenuator is proportional to wedge position and is sensitive to the precision of wedge control. Thus, we propose another dynamic bowtie design called a fluid-filled dynamic bowtie filter (FDBF), a two-dimensional array of small binary elements (filled or empty), that may be more reproducible due to digital control. On average, for simulated scans of chest, abdomen, and shoulder sections of an anthropomorphic phantom, the proposed FDBF reduces the maximum-count-rate required of a PCD to 1.2 Mcps/mm2, which is 55.8 and 3.3 times lower than the max-count-rate of the conventional bowtie and the piecewise-linear bowtie, respectively. For the pulse pileup effect, the performance of several analytical models are dependent on the assumptions used, including the assumed pulse shape which could differ from the actual one. From our sensitivity analysis of a pileup model by Taguchi et al. (Med Phys, 2010), the accuracy of some parameters such as the deadtime are more important than others, and they matter more with increasing count rate. For the bandwidth problem, we explored the use of data compression that could be performed prior to transmission through the slip ring. Utilizing the dependencies in the multi-energy data, our proposed compressor achieves an average compression ratio of 2.25:1 for lossless compression and 4.27:1 for lossy compression.
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Online 9. Concierge 50: Stanford University Press Updates [2019]

Description
Archive/Manuscript
Summary
Join us as we kick off 2019 with a presentation on Stanford University Press. Alan Harvey will give a brief history of the Press and an overview of their operations in Redwood City, with focus on recent developments within the book publishing industry at large. Specific programs, such as the Stanford Briefs, Redwood Press, and supDigital (the Press' new program of interactive scholarly works) will also be explored.
Join us as we kick off 2019 with a presentation on Stanford University Press. Alan Harvey will give a brief history of the Press and an overview of their operations in Redwood City, with focus on recent developments within the book publishing industry at large. Specific programs, such as the Stanford Briefs, Redwood Press, and supDigital (the Press' new program of interactive scholarly works) will also be explored.
Collection
Stanford University Libraries Concierge Project

Online 10. Conformational dynamics and catalytic control of assembly line polyketide synthases [2019]

  • Li, Xiuyuan, author.
  • [Stanford, California] : [Stanford University], 2019.
Description
Book — 1 online resource.
Summary
Polyketides are a large class of natural products with interesting structural scaffolds and diverse biomedical activities. The modular nature of assembly line polyketide synthases (PKSs) has inspired ambitions to realize combinatorial biosynthesis to produce novel polyketide-based chemicals. Meanwhile, the proliferation of putative PKS gene clusters from whole genome sequencing has provided a wealth of potential building blocks. However, the broader adoption of polyketide biosynthetic engineering remains a challenging task. Designer PKS chimeras often fail to produce anticipated products in meaningful titers, reflecting an inadequate understanding into the fundamental biosynthetic logics in wild type PKSs. One hallmark of assembly line PKSs is their ability to invariably catalyze a well-defined sequence of chemical transformations with precise control on product structure and stereochemistry. Such vectorial biosynthesis requires an elaborate control mechanism to channel reactive intermediates along the catalytic cycle. In this dissertation, we seek to develop tools to analyze vectorial biosynthesis of 6-deoxyerythronolide B synthase (DEBS), a prototypical PKS, using a combination of monoclonal antibodies, small molecule activity probes and structural biology techniques. We aim to build the conceptual framework to understand the fundamental enzymology of PKSs, with an emphasis on the conformational dynamics and functional control in the context of catalysis. A major challenge to study PKSs arises from their flexible nature. A minimal functional PKS module consists of at least four distinct catalytic domains connected by flexible linkers. The full DEBS contains six such modules dispersed on three separate homodimeric polypeptide chains. The entire mega-enzyme fits in a cube of roughly 400-500 Å in dimension, where more than twenty enzymatic domains are packed. To address the protein flexibility issues, we have applied three complementary strategies. In Chapter 2, we describe development of monoclonal Fab antibody tools to study the structure and function of DEBS. By use of a fully human naive antigen-binding fragment (Fab) library displayed on a phage library, a number of high-affinity Fabs were identified against almost all the enzymatic domains central to function of DEBS. We examined these Fabs in search of potential binders to trap DEBS in catalytically relevant conformations. In Chapter 3, we describe one such Fab, 1B2, that binds to the N-terminal docking domain of DEBS Module 3. The co-crystal structure was solved to 2.1 Å resolution. Surprisingly, the X-ray crystal structure showed that this Fab locks the Module 3 in an extended conformation. Tandem size-exclusion chromatography small-angle X-ray scattering (SEC−SAXS) revealed that the same extended conformation is maintained in solution phase under conditions that preserves the maximal enzymatic activity. In vitro kinetic analysis proved that this antibody stabilized module conformation was fully competent for catalysis of intermodular polyketide chain translocation as well as intramodular polyketide chain elongation and functional group modification of a growing polyketide chain. Taken together, the extended conformation of a PKS module is fully competent for all of its essential catalytic functions. In Chapter 4, we report another Fab, 3A6 that recognizes the terminal thioesterase (TE) domain. Biochemical assays indicated that 3A6 binding does not inhibit enzyme turnover. The 2.45 Å co-crystal structure model revealed atomic details of the protein-protein recognition mechanism. Fab binding had minimal effects on structural integrity of the TE. In turn, these insights were used to interrogate via small-angle X-ray scattering the solution-phase conformation of 3A6 complexed to a catalytically competent PKS module and bi-module. In Chapter 5, we describe our preliminary results on both negative staining and cryogenic electron microscope. Both Fab-free and Fab-bound DEBS samples have been screened. Best 3D classification result comes from 1B2-Module 2, although sample heterogeneity issues remain. In Chapter 6, we discuss the application of a small molecule activity probe and the discovery of a novel turnstile control mechanism in DEBS catalysis. In summary, this thesis attempts to expand the toolbox to investigate the detailed mechanism of PKS function and control.
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Online 11. Core-shell nanomaterials for enhanced oxygen electrocatalysis [2019]

Description
Book — 1 online resource.
Summary
Fuel cells and electrolyzers are emissions-free, electrochemical devices for the interconversion of electricity and chemical energy that hold significant promise towards clean electrification of the transportation sector and carbon-neutral fuel generation, respectively. Unfortunately, both devices suffer from kinetic limitations of the oxygen electrochemical reactions, resulting in performance inefficiency and high catalyst costs and prompting the search for economical, high-performance oxygen electrocatalysts. Core-shell nanostructured catalysts have the potential to decrease precious metal loading requirements over their monometallic counterparts and improve activity via electronic and geometric modifications induced by the core material. This thesis investigates the benefits of the core-shell electrocatalyst motif for both the oxygen reduction reaction (ORR) and the oxygen evolution reaction (OER) across several materials systems and electrolyte conditions. First, the performance advantages of Pt-based core-shell nanostructured catalysts for the ORR (occurring at the fuel cell cathode) in acidic media is explored. Utilizing a systematic methodology for catalyst design, we identify Ir@Pt (core@shell) nanoparticles as a promising system for enhanced ORR performance, synthesize Ir@Pt core-shell nanoparticles, and demonstrate an activity and stability enhancement over the commercial state-of-the-art Pt/C catalyst. Building on this demonstration of the core-shell catalyst platform, this thesis further explores core-shell materials for the OER (occurring at the electrolyzer anode). Inspired by the established beneficial effects of Au supports for thin-film OER catalysts, Au@metal-oxide nanoparticles were synthesized and characterized for alkaline OER. These mixed-metal oxide catalysts demonstrated a general activity enhancement with the inclusion of a Au-core, illustrating the successful translation of catalyst/support effects to the core-shell nanoparticle architecture. Finally, the last part of this work focuses on further extending the core-shell morphology to the OER in acidic media. A perspective on the past, present, and future state of OER catalysis in acid is first provided to reveal trends and opportunities for improved catalyst design. Finally, investigations of Sr iridate particles and bimetallic Ir-based thin films are presented and catalysts with significantly improved intrinsic activity over pure Ir-oxide are identified. Overall, this work demonstrates the versatility and promise of the core-shell morphology to achieve high performance catalysts across various reactions, electrolytes, and material chemistries.
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Online 12. The delivery of water services through public-private partnerships [2019]

Description
Book — 1 online resource.
Summary
Globally, approximately 1.8 billion people, mainly in low- and middle-income countries, use a source of drinking water that suffers from microbial contamination. This includes piped water supplies (Bain et al., 2014). There exists an urgent need to improve access to water supply services and to replace aging water and sanitation network infrastructure. In an effort to do so, private sector participation, mainly in the form of Public-Private Partnerships (PPPs), has been increasingly used to help improve efficiency, access to, and quality of water services. The first wave of PPPs led by multinational operators was met with a fair amount of backlash. The growth in PPPs since has seen a significant shift towards PPPs led by local private water operators. However, extant research has used theoretical frameworks and constructs that were developed during the multinational era and are failing to explain and predict PPP outcomes today. For the prevailing local-dominated context, a new theoretical framework is developed and suggests more relevant constructs and indicators, such as operator localness, informal renegotiations, and contract transfers, to assess contract fate in water sector public-private partnerships. Grounded theory, cross-case comparison, and fuzzy set Qualitative Comparative Analysis (fsQCA) are used to build theory and suggest potential causal combinations leading to contract persistence and cancellation in water PPPs. Counter to the dominant theory in the literature, the analysis finds that a combination of operator localness, informal contractual supports, and contract transfers impact persistence. The findings build on our understanding of the viability of water PPPs and has implications for structuring, managing, and assessing private sector engagement in water service delivery in low- and middle-income countries. This dissertation focuses on Latin America as it has comparatively high levels of PPP experience globally and has been a focus of extant literature on water PPP renegotiations, cancellations, and performance (Andres, Guasch, Haven, & Foster, 2008; Guasch et al., 2017, 2008, 2003; Marin, 2009a; Marin et al., 2010). Argentina, especially, has implemented an ambitious water PPP program with variation in operator localness and in contract outcomes.
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Online 13. Design and analysis of interactive multi-robot systems without explicit communication [2019]

  • Wang, Zijian, author.
  • [Stanford, California] : [Stanford University], 2019.
Description
Book — 1 online resource.
Summary
The mission of this thesis is to develop decentralized control algorithms that enable intelligent robots to interact with other robots or humans without explicit communication. Study of the interactive behaviors among robots will play an important role for our future society as we expect to have an increasingly large number of robots to serve in people's everyday lives. Unfortunately, most robots today lack awareness and understanding of other surrounding robots or humans and have to be caged or fenced, for example in factories, in order to operate safely. In this thesis, we develop a series of scalable approaches to address how a large swarm of robots cooperate and compete with each other. The first part of this thesis deals with multi-robot manipulation, a cooperative task where a group of robots collaborate to move a common heavy payload. We first propose a decentralized force and torque controller for planar object manipulation that allows many follower robots to synchronize their wrenches to a leader robot, who guides the entire team, using the measurement of the object's motion at their local attachment points. We rigorously prove the convergence guarantee of the controller using nonlinear control theory and Lyapunov style stability arguments. We verify the proposed method in simulations with up to 1000 robots to move various objects such as a simulated piano of realistic size. Two custom robot platforms, the differential-drive m3Pi robot and the omni-directional OuijaBot, are designed and built for experimental validation under real-world noises and disturbances. Next, we extend our planar manipulation to the 3-D space by rigidly attaching a group of quadrotor aerial robots to the payload. We propose a decentralized wrench coordination algorithm that can mathematically guarantee the 6-degree-of-freedom stability of the payload despite the challenge arising from motor saturation. We also provide a trajectory planning pipeline which explicitly accounts for the force/torque input constraint and therefore guarantees feasibility. Both simulations and experiments with quadrotors are performed to show the effectiveness of our approach for multi-robot manipulation in 3-D. The second part of this thesis addresses competition in the context of multi-robot racing. We present a real-time game theoretic planning algorithm for a robotic vehicle to race against multiple opponents on a racecourse. Using a novel iterative best response algorithm, we can find approximate Nash equilibria in the space of the multiple robots' trajectories that account for the opponents' intentions and responses. We also apply machine learning techniques to learn from the historical racing data offline, which can then be used to accelerate and improve the online solution during real-time planning. We conduct extensive simulation studies, and statistics reveal that our game theoretic planner largely outperforms a baseline model predictive controller that does not consider the opponents' responses. Experiments are conducted with four quadrotor aerial robots to validate our approach in real time and with physical robot hardware. All of our proposed algorithms have the feature of using no explicit communication among robots. In multi-robot manipulation, we show that local sensing of the payload's state of motion can acquire enough information for global coordination. In game theoretic planning, robots account for competitors' reactions through intention inference. This feature greatly extends the usability of our approaches when a communication network is unavailable or unreliable among a large swarm of robots.
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Online 14. Design and implementation of tunable diode laser-based multi-species and enthalpy sensing in extreme environments [2019]

Description
Book — 1 online resource.
Summary
A comparison of scanned-DAS and scanned-WMS was completed within the context of a biomass gasification pilot scale facility, while scanned-DAS was implemented and optimized to increase sensing capabilities in the mixing volume (MV) of the 60 MW Interaction Heating Facility (IHF) at NASA Ames Research Center (ARC). In the biomass gasification study, a demonstration of in situ laser-absorption-based sensing of H2O, CH4, CO2, and CO mole fraction is reported for the product gas line of a biomass gasifier. Field measurements were demonstrated in a pilot scale biomass gasifier at WestBiofuels in Woodland, California. The performance of a prototype sensor was compared for the two sensing strategies, scanned-DAS and scanned-WMS. The lasers used had markedly different wavelength tuning response to injection current, which led to establishing guidelines for laser selection for sensor fabrication. The complications of using normalized WMS for relatively large values of absorbance and its mitigation are discussed. The laser absorption sensor provided measurements with the sub-second time resolution needed for gasifier control and more importantly provided precise measurements of H2O in the gasification products, which can be problematic for the typical gas chromatography sensors used by industry. The IHF at NASA ARC is a critical facility used to study and characterize thermal protection systems (TPS) of reentry spacecraft. The IHF generates an electrical arc to energize room temperature air, which is then forced through a converging-diverging nozzle. Material and model test pieces are then subjected to the stagnation environment of the flow stream. The efforts at ARC focused on characterizing the mixing of add-air in the MV of the IHF. Conditions in the IHF, in the mixing volume (MV) where this study focused its optical measurements, range from 5,000 to 7,000 K and 1 to 9 atm. Path-average line-of-sight measurements of temperature and enthalpy were inferred using an electronic atomic oxygen transition near 777 nm. The scanned-DAS sensor was optimized to capture high add-air and high-pressure conditions that previously had not been measurable. Optimization of the sensor allowed for fully resolved absorbance profile measurements at the maximum pressure test condition in the IHF MV. Enhanced sensor capabilities confirmed uniform flow and flat temperature immediately upstream of the arcjet's converging-diverging nozzle inlet. Less uniform and parabolic temperature profiles were observed immediately downstream of add-air injection. This arcjet facility implements injection of room temperature air, i.e. add-air, to tune the bulk and centerline enthalpy generated at the nozzle exit. Centerline temperatures at an axial location downstream of add-air injection confirmed the need for mixing beyond the MV entrance. Enthalpy measurements ranged from 16 to 27 MJ/kg and are in agreement with the IHF's current enthalpy measurement methods. This confirmed the observed reduction in achievable enthalpy after installation of the MV. Centerline measurements quantified the mixing process for various add-air conditions indicating an opportunity for enthalpy recapture. Axial locations of sufficient mixing were identified and provide a potential for reduction of the MV length and thus improved facility performance. Optimization of this sensor will enable future use by non-experts to provide critical data on the arcjet environment in the IHF, thereby enhancing arcjet test results and leading to greater reliability of spacecraft TPS designs.
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Online 15. Design optimization of highly flexible aircraft with aeroelastic constraints [2019]

  • Variyar, Anil, author.
  • [Stanford, California] : [Stanford University], 2019.
Description
Book — 1 online resource.
Summary
With the need to drastically reduce aircraft emissions and fuel burn, there have been significant strides towards the design of fuel-efficient aircraft. This has involved moving towards extremely high aspect-ratio wings that need to be aeroelastically tailored and unconventional aircraft configurations. However aeroelastic stability of such configurations is a major challenge. In order to ensure that the fuel-burn improvements predicted in the conceptual or early preliminary design phase are attained in reality, it is essential to ensure that aeroelastic constraints are enforced early on in the design phase itself. However inexpensive yet accurate computation of transonic aeroelasticity especially transonic flutter predictions is quite a challenge due to the non-linearity in the flow at transonic regimes which requires non-linear fluid dynamics approaches that are generally too expensive for the early design phases. In this work we attempt to address this issue by first developing a two-dimensional parametric transonic low-order model that accurately predicts unsteady flow results for airfoils. A set of airfoil agnostic parameters for this model are obtained that permit accurate two-dimensional transonic aeroelastic simulations. This approach is then extended into three dimensions using the ASWING Weissinger model formulation. Next a set of in-house capabilities are developed that permit the inclusion of this approach into a conceptual design loop. Finally a number of flutter constrained optimizations are performed to understand the impact of imposing flutter constraints in an aircraft design/sizing loop.
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Online 16. Developing angular intensity correlations of X-ray photons as a tool for studying structures of proteins in non-crystalline solutions [2019]

  • Qiao, Shenglan, author.
  • [Stanford, California] : [Stanford University], 2019.
Description
Book — 1 online resource.
Summary
This dissertation offers lessons learned and tools developed as we attempt to apply correlated X-ray scattering (CXS) to non-crystalline proteins in solution. It builds on our previous work of extracting correlation signals from scattering intensities of ensembles of mental nanoparticles, which has led to three-dimensional (3D) structural insights not reflected in azimuthally averaged measurements. In his 1977 paper, Zvi Kam proposed the idea of correlating X-ray photons scattered by an ensemble of randomly oriented particles suspended in solution. He found that if the exposure time is much shorter than the diffusion timescale of Brownian motion, correlations between photons scattered into different angles encode 3D structural information of the particles not accessible via conventional small or wide-angle X-ray scattering. The advent of the X-ray free electron laser (XFEL) renders Kam's idea feasible for non-crystalline solutions of proteins. With femtosecond pulses and extremely high fluences, the XFEL is not only capable of probing ensembles of molecules essentially frozen in time but also delivering a large number of photons per pulse, a capability critical for enhancing angular intensity correlation signals. Meanwhile, probing proteins in solution removes the need for crystallization, allows measurements of mixtures of conformational states under physiological conditions, and broadens opportunities for time-resolved experiments. The body of work in this dissertation draws from scattering data collected with samples containing the G-protein Gi alpha subunit during two separate beam times conducted at the Linac Coherent Light Source. The Gi alpha subunit was chosen for these proof-of-principle experiments because of its important role in the G-protein coupled receptor signaling pathway. This dissertation has taken the first steps in developing and validating CXS as a tool for probing ensembles of biomolecules in solution. These first steps as well as ideas described in this dissertation to improve CXS towards a mature pipeline that yields reliable and detailed structural insights aim to inspire others in the solution scattering community to engage with the unique challenges and rewards of this technique.
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Online 17. Development and application of coupled K-feldspar PB isotopic and 40AR/39AR methods to reconstruct late cretaceous/cenozoic deformation of the California margin [2019]

Description
Book — 1 online resource.
Summary
The evolving plate boundary along the California margin over the last 100 m.y. has dramatically impacted the geologic evolution of the western United States. Laramide flat-slab subduction extinguished Sierra Nevada arc magmatism as trench-derived sediments (i.e., Rand and related schists) were underthrust and accreted at 25-30 km depth beneath the southernmost Sierra Nevada and NW Mojave Desert (SSN/MD) during the Late Cretaceous. During this time, the southern California forearc margin was severely disrupted. Breachment of the mid-Cretaceous batholith in the southern California region ultimately permitted depositional systems to extend eastward and permit extraregional sediment from the continental interior to reach the margin during the Eocene. Subsequently, between 30-25 Ma, the North American and Pacific plate boundary was established. The resulting development of a northwest-propagating transform margin produced "slab gaps" beneath the SSN/MD that triggered mantle upwelling, volcanism, and extension of the crust. Each of these significant changes has imprinted a thermal history record in the SSN/MD crust that can be interrogated through integrated detrital and basement thermochronology. Modal detrital phases such as K-feldspar can yield significant thermal history and provenance information but have been under-utilized. The benefits of using K-feldspar in detrital studies are twofold: K-feldspar 40Ar/39Ar has shown promise as both a basement and detrital thermochronometer. Moreover, its propensity to incorporate common Pb into its crystal structure allows its Pb isotope composition to be used as a provenance tool. The well-established extreme variation in Pb isotopic values and thermal fingerprints of tectonic processes across the western United States can be exploited to reconstructing the southern California margin. In this dissertation, I develop and apply basement and detrital K-feldspar coupled 40Ar/39Ar and Pb isotopic analysis to evaluate the Late Cretaceous/Cenozoic evolution of the California margin. In Chapter 1, I demonstrate viability of K-feldspar coupled 40Ar/39Ar and Pb isotopic analysis by quantitatively investigating the effects of laser fusion during 40Ar/39Ar analyses of K-feldspar upon subsequent LA-ICP-MS measurement of Pb isotopic ratios. I also show the feasibility of using LA-ICP-MS to generate statistically significant datasets. In Chapter 2, I describe how I have developed a regionally extensive database of new Pb isotopic values in K-feldspar for the southwestern United States basement. I furthermore evaluate the utility of this database by demonstrating how it can be applied to evaluate paleodrainage evolution during the early Eocene to early Miocene along the SSN/MD margin. In Chapter 3, I develop a database of new 40Ar/39Ar thermal history results from mid-Cretaceous plutonic rocks throughout the SSN/MD region. I also develop single-crystal incremental heating methods to detrital K-feldspar from derivative Eocene-Miocene strata. Coupled interpretation of the basement and detrital results is used to assess the Late Cretaceous thermal evolution of the SSN/MD region. Collectively, these results constrain the magnitude and timing of Laramide subduction refrigeration of the southern California margin. Unimodal and identical detrital K-feldspar age distributions and thermal histories from the forearc strata confirm subduction refrigeration extended into the shallow crust and affected a broad region of the Mojave Desert province. Final exhumation of the deepest rocks in the western Mojave in the early Miocene was ultimately due to northwestward migration of the Mendocino triple junction along the California margin. Collectively, these case studies demonstrate how these new analytical and interpretative methods can be profitably applied to future regional deformation and tectonically driven re-organization of drainage patterns.
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Online 18. Development of a quantum-based superconducting radio-frequency voltage standard [2019]

Description
Book — 1 online resource.
Summary
Metrology science is continuously transitioning toward a paradigm in which standard definitions of SI units are represented by systems that use quantum mechanical effects to relate measurement units to fundamental constants. This dissertation describes research efforts to achieve this transition for voltage and power metrology at frequencies above the audio range. In particular, this dissertation presents the design and experimental testing of a superconducting programmable radio-frequency waveform synthesizer intended for quantum-based metrology applications. The waveform synthesizer incorporates high-speed active superconducting circuit elements known as Josephson junctions and produces output waveforms with spectral power distributions that are traceable to the values of fundamental constants. This synthesizer has practical applications for calibration and characterization of communications-frequency electronics, and will supplement existing radio-frequency metrology tools that are not quantum-based.
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Online 19. A discontinuous galerkin method with enrichment for boundary layers [2019]

Description
Book — 1 online resource.
Summary
A discontinuous Galerkin method with enrichment and Lagrange multipliers (DGLM) is proposed for the solution of problems with boundary layers. Specifically, this includes the steady and unsteady advection-diffusion equation with a spatially-varying advection field and the steady incompressible Navier-Stokes equations. The standard finite element method (FEM) is susceptible to the issue of spatial instability at practical mesh resolutions, typically observed as non-physical oscillations in the numerical solution to these problems. This is especially the case in the advection-dominated regime in which the boundary layers have steep gradients. Like the discontinuous enrichment method (DEM), the DGLM overcomes this issue through the use of novel shape functions designed to resolve boundary layers. These are chosen here element-wise as polynomials that are additively enriched with approximate free-space solutions of the governing differential equation. The enrichment functions are inspired by the boundary layer theory and are derived using an asymptotic analysis for different types of boundary layers. Inter-element solution continuity is weakly enforced using polynomial Lagrange multipliers. The method is shown to be stable in the inf-sup sense. Numerical results reveal that the DGLM has a lower error constant than the FEM and outperforms it for both the advection-diffusion equation in the high Peclet number regime and the incompressible Navier-Stokes equations in the laminar flow regime.
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Online 20. The discovery and design of bivalent, small-molecule glucose-6-phosphate dehydrogenase activators and tetramethyleneethane equivalents for the convergent synthesis of the bicyclo[4.4.0]decane core [2019]

Description
Book — 1 online resource.
Summary
This dissertation covers work carried out independently in both the Mochly-Rosen and Wender Labs. Chapters 1 and 2 focus on the relevant background and development of a novel class of enzyme activators to treat G6PD deficiency (Mochly-Rosen Lab). Chapter 3 (Wender Lab) focuses on the development of novel synthetic methods for the construction of the bicyclo[4.4.0]decane core. The application of this method in the construction of novel dyes is outlined. Chapter 1 provides a historical perspective on the discovery of mutated glucose-6- phosphate dehydrogenase (G6PD) as the underlying cause of favism and related diseases (e.g. primaquine sensitivity). A discussion follows which highlights certain pathologies associated with G6PD deficiency along with the consequences of reduced NADPH synthesis. The tertiary and quaternary structure of G6PD is discussed along with the functional consequences of altering the oligomeric state of the enzyme. Chapter 2 begins with background on small-molecule activators and protein-protein interaction (PPI) stabilizers. The high-throughput screening (HTS) campaign to find a small- molecule activator of G6PD is described, followed by a mechanistic investigation of the initial 'hit' molecule, AG1. This mechanistic understanding enabled the design of new analogs without the reactive liability of AG1 (disulfide) and led to the understanding of the general pharmacophore of these compounds. A discussion of the relevant synthetic methods and properties of these molecules is presented. Chapter 3 details the development of a novel class of reagents which enable two conjunctive cycloadditions for the synthesis of the bicyclo[4.4.0]decane core (naphthalene, higher acene and heterocyclic products). This class of reagents is a synthetic equivalent to the tetramethyleneethane (TME) diradical. These reagents use the vinylogous Peterson elimination for reactivity generation after the first cycloaddition between a dienophile and the novel diene. One reagent, DMTB, was found to enable the construction of bicyclic systems resulting from all thermal Diels-Alder (DA) cycloadditions or a mixture of DA cycloadditions followed by a transition-metal-catalyzed [4+2] reaction. Ultimately, DMTB was used in the synthesis of a new solvatochromic dye, 6-DMA in 69% overall yield. To enable back-to-back transition- metal-catalyzed [4+2] products, another reagent (THP-DMTB) had to be utilized due to decomposition of the original reagent under these conditions. In order to enable the formal synthesis of hetero-Diels-Alder products, AcDMTB was developed, which expands the methodology outside the constraints of Diels-Alder or metal-catalyzed cycloadditions.
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