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Title: NON-DESTRUCTIVE CANCER DETECTION IN LYMPH NODE USING PAIRED-AGENT MOLECULAR IMAGING
Creator: Li, Chengyue
Date: 2020
Description: Identification of cancer spread to tumor-draining lymph nodes through lymph node dissection and histology offers critical information for...
Show moreIdentification of cancer spread to tumor-draining lymph nodes through lymph node dissection and histology offers critical information for guiding treatment in many cancer types, including breast, melanoma, head and neck, lung and gynecologic cancers, as the lymphatic system serves as the primary route for metastasis. Lymph node biopsy involves localization of tumor-draining lymph nodes, followed by their surgical removal and histological assessment. However, the procedure is associated with overtreatment concerns and some considerable morbidity, including lymphedema, seroma formation, and restricted arm movement. Moreover, conventional histological analyses are time-consuming and laborious, yet pathologists generally examine less than 1% of the volume of each lymph node, leading to undetected micrometastasis (tumor clusters 0.2-2mm in diameter) in 30-60% of cases. In response to these limitations in standard lymph node dissection protocol, there is a significant need for the development of lymph node imaging strategies that are capable of identifying metastatic cancer as a means of staging a patient’s cancer without the need for invasive and time-intensive conventional pathology. Paired-agent imaging molecular imaging protocols have been spearheaded by our group and entail co-administration of a control imaging agent with a molecular targeted agent as a way to account for nonspecific uptake and retention. The overall goal of my thesis was to methodically design, optimize and evaluate the clinical utility of a paired-agent lymph node imaging protocol to achieve levels of sensitivity and specificity in nodal staging not possible with current conventional methods, less invasively and at a fraction of the time and cost.
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Title: A Multi-level Data Integration Approach for the Convergence of HPC and Big Data Systems
Creator: Feng, Kun
Date: 2020
Description: HPC is moving towards exascale (10^18 operations per second) following the trend that has continued for over half a century. Such an extremely...
Show moreHPC is moving towards exascale (10^18 operations per second) following the trend that has continued for over half a century. Such an extremely compelling computing power brings huge opportunities for scientists to explore their problems with larger sizes and finer granularity. As a result, the data volume produced and consumed by extreme-scale computing has increased dramatically. To gain useful scientific insights, scientists analyze tremendous amounts of data, which stresses the storage systems and requires efficient data access. Besides the data volume increase, the variety of I/O subsystems grows as well to meet the drastically different, often conflicting I/O requirements of numerous applications. HPC and BD, as two major camps of extreme-scale computing, have been developed separately for a long time and diverged from computing and storage paradigms. However, recent developments have proven the convergence of them leads to more efficient scientific output. Hence, unification between these ecosystems is necessary to accelerate extreme-scale computing with the collaboration of applications from both camps. Therefore, integrated I/O has become a major issue that needs to be addressed as the extreme computing community moves forward.This study explores improvement by proposing a new integrated data access system for extreme-scale computing. We enhance the BD framework to adapt to the change of integrated data access requirement by enabling direct processing of scientific data from PFS at the HPC site. Our framework can perform up to 8x faster than the state-of-the-art solutions in representative workloads. We design a new advanced I/O middleware service to utilize data aggregation resources to facilitate integrated data access in scientific workflows with both HPC and BD applications. Our middleware service can reach up to 10x speedup against the default solution and 133% better performance than existing solutions. We propose a novel storage integration solution on the storage side to unite all the storage resources, to unify the namespace across all the storage systems, and provide an ultimate integrated data access service. The integrated solution can speed up a real workflow with integrated data access requirements by up to 6.86x over existing solutions. The three-level integration at the application level, middleware level, and storage level provide us a systematic hierarchical I/O integration. Our implementation results show that the three-level optimized design and implementation is feasible and effective. It improves the state-of-the-art solutions and helps us to achieve an enhanced I/O system towards extreme-scale computing to support both HPC and BD applications.
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Title: Effect of Phosphorus Additions on Polycrystalline Ni-base Superalloys
Creator: Li, Linhan
Date: 2020
Description: In recent years, advanced polycrystalline Ni-base superalloys have been developed with elevated levels of γ′ forming elements and high level...
Show moreIn recent years, advanced polycrystalline Ni-base superalloys have been developed with elevated levels of γ′ forming elements and high level of refractory elements as solid-solution strengtheners in an effort to extend the temperature capability. Moreover, the properties of the grain boundaries become more important and this necessitates the need to study of effects of minor additions of interstitial P for grain structure optimization. Due to the increased level of refractory elements employed, powder-processed Ni-base superalloys tend to have a high propensity to form Topologically Close-Packed (TCP) phases, which was found to be further promoted by the addition of P. A systematic study of the phase stability of high refractory content powder-processed Ni-base superalloys with three levels of P additions revealed an increased tendency to form Laves phase as a function of P additions. Additions of P were discovered to not only depress the incipient melting temperature to stabilize the eutectic Laves phase, but also promote Laves phase formation during the aging heat treatment and the following isothermal exposure. During the thermal exposure, excessive formation of Laves phase promoted the formation of a basket-weave structure comprised of an intertwined mixture of Laves and Sigma phase. The stabilization of the Laves phase structure due to P additions was found to be consistent with Density Functional Theory (DFT) calculations and could be rationalized through structure maps that relate the valence electron concentration and relative size differences. Additionally, a variation of grain structure obtained via either a sub-solvus or super-solvus solution heat treatment was noted to some extent vary the P segregation level at high-angle grain boundaries, thereby affecting the phase stability. For a sub-solvus solutioned grain structure that possessed a high length density of high-angle grain boundaries, the Laves phase formation was depressed for alloys with a low level of P addition. However, the phase stability variation associated with Laves phase formation was moderate when high concentrations of P were present. The effect of P addition on the γ′ microstructure variation is limited, which was confirmed by microstructure observations as well as through the short-term 0.6%-strain stress relaxation tests at high temperature. Heat treatment variations to modify the secondary and tertiary γ′ microstructures were discovered to exert a much more significant influence on the 0.6%-strain stress relaxation behavior. When a higher initial strain of 2% was applied, the stress relaxation behavior of the powder-processed Ni-base superalloys was found to be microstructure independent. The creep ductility of Waspaloy was determined to be notably reduced by the P additions due to the enhanced precipitation of M23C6 carbide at the grain boundaries. Excessive precipitation of M23C6 carbide increased the likelihood of brittle fracture when tested under low temperature/high stress creep conditions. However, the P addition as well as the excessive precipitation of M23C6 carbide did not impact the creep behavior as the dominant deformation was transgranular in nature when tested under high temperature/low stress conditions.
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Title: ATOMIC LAYER DEPOSITION STUDIES OF GOLD AND TUNGSTEN DISULFIDE
Creator: Liu, Pengfei
Date: 2020
Description: In the last few decades, atomic layer deposition (ALD), as a vapor deposition technique and a powerful thin film fabrication method, has...
Show moreIn the last few decades, atomic layer deposition (ALD), as a vapor deposition technique and a powerful thin film fabrication method, has received more and more attention in many fields. A variety of materials can be made by ALD; however, the progress of ALD application is still necessary. Meanwhile, in the process of film fabrication by ALD, the interfacial chemistry is interesting and well worth studying. This dissertation mainly described the process of exploring two materials, gold and tungsten disulfide, fabrication and related content.For the portion of applying ALD in gold thin film deposition, a relatively comprehensive process was explored, studied, analyzed and discussed. Start with the synthesis of the gold precursor, Me2Au(S2CNEt2), the synthetic reaction was explored. By modified the conditions, such as solvent system, twice the yield as previously reported in the literature were achieved. Next, the application of in situ microbalance and infrared spectroscopic technique illuminate the organometallic chemistry during the gold thermal ALD process with Me2Au(S2CNEt2) and ozone. In situ quartz crystal microbalance (QCM) studies give an explanation for the nucleation delay and island growth of gold on a freshly prepared aluminum oxide surface. In situ infrared spectroscopy provides insight to study the surface chemistry during the process, which supports an oxidized gold surface mechanism. The epitaxy of gold thin film was explored by X-ray diffraction. The thermal ALD gold on various substrates reveals out-of-plane orientation, however, in-plane orientation was only existed in the gold film on mica. For the portion of applying ALD in tungsten disulfide fabrication, the early work started with studying the effect of interfaces upon crystallinity. The sulfuration of indium thin film with different interface was explored. Then the idea of “interfaces” was brought into the process of tungsten compounds fabrication. Due to this “indirect” method which made tungsten disulfide by sulfurizing ALD made tungsten compounds (eg. tungsten oxide and tungsten nitride) could not reduce the reaction temperature of tungsten disulfide synthesis to less than 400 °C. Sequently, the “direct” way of tungsten disulfide fabrication which directly utilized tungsten precursor and H2S in ALD system was tested and explored. With the tungsten precursors developed by our group, finally, tungsten disulfide could be fabricated at the temperature as low as 125 °C.
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Title: Resilience Enhancement of Critical Cyber-Physical Systems with Advanced Network Control
Creator: Liu, Xin
Date: 2020
Description: Critical infrastructures are the systems whose failures would have a debilitating impact on national security, economics, public health or...
Show moreCritical infrastructures are the systems whose failures would have a debilitating impact on national security, economics, public health or safety, or any combination of those matters. It is important to improve those systems' resilience, which is the ability to reduce the magnitude and/or duration of disruptive events. However, today’s critical infrastructures, such as electrical power system and transportation system, are deploying advanced control applications with increasing scale and complexity, which leads to the migration of their underlying communication infrastructures from simple and proprietary networks to off-the-shelf network technologies (e.g., IP-based protocols and standards) to handle the intensive and heterogeneous traffic flows. On one hand, this migration provides an opportunity for both academic and industry communities to develop novel ideas on top of existing schemes; on the other hand, it exposes more vulnerabilities for cyber-attacks. Moreover, since the large-scale power system may choose leased networks from Internet service providers (which is a critical infrastructure itself), there exists an interdependency relationship between power and communication infrastructures, where the power transmission control requires message delivery services while the network devices rely on the power supply. These problems raise research challenges to improve the system resilience of critical cyber-physical systems.In this thesis, we focus on resilience enhancement of critical infrastructures from the communication network's aspects. The application domain includes both power and transportation systems. For power systems, we first apply advanced network control techniques (i.e., software-defined network (SDN) and fibbing control scheme) in the transmission grid communication network to improve the grid status restoration process under network failures and cyber-attacks. We develop a unified system model that contains both transmission grid monitoring system (i.e., phasor measurement unit (PMU) network) and communication network, and formalize a mixed-integer linear programming (MILP) problem to minimize the recovery time of system observability with the power and communication domain constraints. We evaluate the system performance regarding the recovery plan generation and installation using IEEE standard systems. However, the advanced network-based control scheme could also lead to problems, since it requires a power supply for the network devices. Thus, we investigate the interdependency relationship between the power grid and communication network and its impact on system resilience. We conduct a survey work that summarizes existing research based on two dimensions: objectives (i.e., failure analysis, vulnerability analysis, failure mitigation, and failure recovery) and methodologies (i.e., analytical solutions, co-simulation, and empirical studies). We also identify the limitations of existing works and propose potential research opportunities in this demanding area. Lastly, based on the review work, we conduct research that focuses on fast power distribution system restoration that involves interdependency constraints. When a natural disaster happens, both power and communication components might be damaged. Furthermore, since they are dependent on each other's service to function correctly, the failures may propagate to the hardware/software that are not affected initially. In this work, we focus on the recovery stage where the failed components in the system are already fully detected and isolated. We construct a mathematical model of the co-existing power and communication system and use optimization techniques to produce a crew dispatch plan that restores power as fast as possible by coordinating damage repairing, switch operation, and communication supply processes. We evaluate the restoration efficiency on the IEEE standard system using both analytical analysis and discrete-event simulation.For the second application domain, railway transportation system, we focus on evaluating the resilience of its communication system that exchanges control and monitoring messages with both on-board driver cabin and remote control center. We use advanced discrete-event simulation techniques to achieve a high-fidelity model of the network which makes the evaluation more concrete and realistic. For the Ethernet-based on-board train communication network (TCN), we develop a parallel simulation platform according to the IEC standard and use it to conduct a case study of a double-tagging VLAN attack on this control network. Another component of the railway communication system is the train-to-ground network that enables the communication between the driving system on the train and the control center that issues commands such as the movement authority messages. We customize the NS3 network simulator to model the LTE-based protocol with a real high-speed train trace dataset from public sources. We evaluate the resilience of the cellular network specifically on the handover process, which happens when the train travels from one base station to another. Due to the high-speed nature, the handover success rate is impacted and there are many protocol-based solutions proposed in this research area. We use the high-fidelity simulation model to evaluate some of them and compare the pros and cons.
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Title: The role of fibrillar collagen in tissue function
Creator: Ma, Yin
Date: 2020
Description: Fibrillar collagen plays an important role in maintaining soft tissue integrity and providing chemical and physical cues for cell fate...
Show moreFibrillar collagen plays an important role in maintaining soft tissue integrity and providing chemical and physical cues for cell fate decisions. Collagen remodeling, which alternates the amount, distribution, and biomechanics of collagen, primarily type I (COLI) and type III (COLIII), can change tissue properties. This process is essential not only in biological developments but also in pathological processes. Thus, it is meaningful to understand the correlation between collagen remodeling and tissue dysfunction and investigate the cells' response to fibrous protein matrices. However, current studies in biochemical analysis of collagen and biomechanical study of tissues were carried out at different scales. So it is hard to correlate the data to draw solid conclusions. In this thesis research, we used two collagen disorder associated pathological conditions, pelvic organ prolapse (POP) and micropapillary serous carcinoma (MPSC) of the fallopian tube, as models to unravel the correlation between tissue dysfunctions and the impaired microenvironment relevant to the composition, nanostructure, and biomechanics of a collagen fibril. In the case of POP, we found the collagen fibers in tissues of POP patients were less abundant but stiffer than those of non-POP individuals, implying a loose and fragile matrix that is weakly integrated with other components of the connective tissue to provide adequate support of the pelvic organs. On the other hand, the collagen D-period, the characteristic banding feature which signals the proper assembly of collagen molecules, decreased in POP tissues. We surmised that the molecular level changes of collagen in POP were accountable for the weak matrix mechanics, verified by a systematic in vitro study. We also examined the collagen matrix alternation in MPSC of the fallopian tube, which is thought to cause ovarian cancer via metastasis. Since cancer metastasis is often related to collagen remodeling, we examined the collagen matrix alternation in this disease. We observed the heterogeneous distribution of COLI and COLIII in the papillae of the tumor tissue. Noticeably, COLI was accumulated at the papillae tip, whereas COLIII was dominant at the papillae base. We also observed the absence of collagen matrix between the micropapillary tip and the fibrosis base. Such an uneven collagen distribution implies that the matrix exerted distinctive forces on the tumor cells to regulate their behaviors, including cell migration, directional growth, and shedding from the primary tumor to initiate metastasis. These conclusions have been supported by the results of our in vitro experiments. In investigating the effect of the microenvironment on cell behavior, we established and validated an AFM-based method to collect and quantitatively analyze the mRNA samples from targeted live cells at the single-cell level. This method overcomes issues, such as severe cell damage or even cell death, the capability of time-dependent and in situ analyses, in current methods. The application of the method in studying heterogeneous gene expression in single cells and the interaction between cancer cells and cancer-associated fibroblasts was demonstrated. We also demonstrated that this method can be potentially used to quantitatively analyze the gene expression level changes in a targeted cell in response to the microenvironment.
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Title: FEARING FORGETTING? DEVELOPMENT OF A SCALE TO ASSESS ATTITUDES ABOUT DEMENTIA IN THE LAY POPULATION
Creator: Ogu, Precious N
Date: 2020
Description: Individuals with dementia show a progressive decline in cognitive functioning which results in an inability to complete activities of daily...
Show moreIndividuals with dementia show a progressive decline in cognitive functioning which results in an inability to complete activities of daily living (American Psychiatric Association, 2013). Early diagnosis of dementia is a positive prognostic indicator (World Alzheimer Report, 2011) and is widely regarded as an important pre-condition for improving dementia care (Kim et al., 2015; Vernooij-Dassen et al., 2005). However, negative attitudes and stigma towards dementia could possibly interfere with an individual’s willingness to recognize or accept the idea of themselves having the disease through label avoidance. The goal of the present study was to contribute to understanding the perception of dementia by developing a quantitatively derived and psychometrically validated measure that encompasses the positive and negative attitudes towards dementia held by people without dementia. This study also explored the potential association between negative attitudes about dementia and lack of familiarity with dementia as familiarity with individuals with mental illness is related to stigmatizing attitudes towards mental illness. These goals were achieved by a principal components analysis (PCA) of 56 modified items from extant and well-validated mental illness attitude scales (Community Attitudes to Mental Illness, CAMI, Taylor & Dear, 1981; Social Distance Scale, SDS, Link, 1986; Depression Stigma Scale, DSS, Griffiths et al., 2004). Convergent validity was assessed by examining the relationship between the final derived measure and a construct associated with negative attitudes about mental illness (Mental Retardation Attitude Inventory-Revised, MRAI-R). Discriminant validity was assessed by examining the relationship between the final measure and a construct that should be unrelated to negative attitudes about mental illness (Belief in a Just World Scale, BJW). Finally, exploratory analyses were conducted to assess if attitudes measured by the newly created scale are related to participants’ familiarity with dementia (Level of Familiarity Scale, LoFS, Corrigan et al., 2001). 400 adults with no history of dementia were recruited through Amazon’s MTurk. Participants were compensated by a credit to their Amazon account upon completion of the survey. The PCA supported 2 conceptually different (not method variance) latent components titled Negative Attitudes and Positive Attitudes. These 2 components comprise the Attitudes to Dementia Inventory (ADI). Construct validity was partially supported for each component of the ADI. Degree of familiarity with dementia was not associated with negative or positive attitudes about dementia. Overall, this study is an important contribution to dementia attitudes research. Given the identification of Negative Attitudes and Positive Attitudes have been identified as distinct dimensions of dementia attitudes, the ADI can be used to further investigate how negative reactions towards dementia might cause delays in initiating medical intervention and treatment, and also to examine whether positive attitudes provide any protections against the probable effects of negative attitudes on stigma and help-seeking behaviors. Since the early recognition and diagnosis of dementia is widely regarded as an important condition for improving dementia care (Kim et al., 2015; Vernooij-Dassen, et al., 2005), the ADI can be used to inform stigma-prevention, which hopefully translates into improved help-seeking behaviors.
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Title: Ink drawing, 1975
Creator: Henry, Mary Dill, 1913-2009
Date: 1975-07-07
Description: Untitled drawing by Mary Henry, accompanied by mathematical calculations.
Collection: Mary Dill Henry Papers, 1913-2021

Title: Pencil Drawing on Tissue, undated
Creator: Henry, Mary Dill, 1913-2009
Description: Untitled pencil drawing on tissue paper by Mary Henry, date unknown.
Collection: Mary Dill Henry Papers, 1913-2021

Title: Ink and Colored Pencil Drawings, undated
Creator: Henry, Mary Dill, 1913-2009
Description: Untitled drawings by Mary Henry, date unknown.
Collection: Mary Dill Henry Papers, 1913-2021

Title: Ink and pencil sketches, undated
Creator: Henry, Mary Dill, 1913-2009
Description: Untitled ink and pencil sketches by Mary Henry, date unknown.
Collection: Mary Dill Henry Papers, 1913-2021

Title: Ink and Colored Pencil Drawings, undated
Creator: Henry, Mary Dill, 1913-2009
Description: Untitled drawings by Mary Henry, date unknown.
Collection: Mary Dill Henry Papers, 1913-2021

Title: Pencil Drawing on Tissue, undated
Creator: Henry, Mary Dill, 1913-2009
Description: Untitled pencil drawing on tissue paper by Mary Henry, date unknown.
Collection: Mary Dill Henry Papers, 1913-2021

Title: Ink Drawings, undated
Creator: Henry, Mary Dill, 1913-2009
Description: Untitled drawings by Mary Henry, date unknown.
Collection: Mary Dill Henry Papers, 1913-2021

Title: Colored Pencil Drawings, undated
Creator: Henry, Mary Dill, 1913-2009
Description: Untitled colored pencil drawings by Mary Henry, date unknown. Inscription on verso: "William Winter Comments, PO Box 817, Sausalito"
Collection: Mary Dill Henry Papers, 1913-2021

Title: Colored Pencil Drawings, undated
Creator: Henry, Mary Dill, 1913-2009
Description: Untitled colored pencil drawings by Mary Henry, date unknown. Inscription on verso: "William Winter Comments, PO Box 817, Sausalito"
Collection: Mary Dill Henry Papers, 1913-2021

Title: Colored pencil drawing, undated
Creator: Henry, Mary Dill, 1913-2009
Description: Untitled colored pencil drawing by Mary Henry, date unknown.
Collection: Mary Dill Henry Papers, 1913-2021

Title: Pencil drawing, undated
Creator: Henry, Mary Dill, 1913-2009
Description: Untitled drawing by Mary Henry, date unknown.
Collection: Mary Dill Henry Papers, 1913-2021

Title: Ink drawing, undated
Creator: Henry, Mary Dill, 1913-2009
Description: Untitled drawing by Mary Henry, date unknown.
Collection: Mary Dill Henry Papers, 1913-2021

Title: Ink drawing, undated
Creator: Henry, Mary Dill, 1913-2009
Description: Untitled drawing by Mary Henry, date unknown.
Collection: Mary Dill Henry Papers, 1913-2021

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