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Title: Voxel Transformer with Density-Aware Deformable Attention for 3D Object Detection
Creator: Kim, Taeho
Date: 2023
Description: The Voxel Transformer (VoTr) is a prominent model in the field of 3D object detection, employing a transformer-based architecture to...
Show moreThe Voxel Transformer (VoTr) is a prominent model in the field of 3D object detection, employing a transformer-based architecture to comprehend long-range voxel relationships through self-attention. However, despite its expanded receptive field, VoTr’s flexibility is constrained by its predefined receptive field. In this paper, we present a Voxel Transformer with Density-Aware Deformable Attention (VoTr-DADA), a novel approach to 3D object detection. VoTr-DADA leverages density-guided deformable attention for a more adaptable receptive field. It efficiently identifies key areas in the input using density features, combining the strengths of both VoTr and Deformable Attention. We introduce the Density-Aware Deformable Attention (DADA) module, which is specifically designed to focus on these crucial areas while adaptively extracting more informative features. Experimental results on the KITTI dataset and the Waymo Open dataset show that our proposed method outperforms the baseline VoTr model in 3D object detection while maintaining a fast inference speed.
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Title: Ultrasound Image Guided Robot Arm for Targeted Delivery of Therapeutic Drugs and MicroRNA for Cancer Therapy
Creator: Nagarajan Parimala, Abishek
Date: 2024
Description: Molecular imaging has revolutionized medical diagnostics by providing detailed insights into biological processes at the molecular level...
Show moreMolecular imaging has revolutionized medical diagnostics by providing detailed insights into biological processes at the molecular level within the living subject. Ultrasound Molecular Imaging (USMI) has emerged as a promising diagnostic imaging modality by utilizing targeted contrast agents to unveil crucial molecular information, including vascular biomarkers associated with cancer and other diseases. Despite its potential, the transition of Ultrasound Contrast Agents (UCA) from preclinical evaluation to FDA-approved clinical use faces challenges due to the short in vivo half-life of Micro-Bubbles (MBs), necessitating repeated administrations for comprehensive assessments. Moreover, conventional ultrasound imaging methods suffer from limited scanning areas and single-target focus, leading to low throughput in preclinical evaluations.This thesis addresses these challenges by proposing a robot-assisted whole-body scanning pipeline for preclinical evaluations in Ultrasound Molecular Imaging. By integrating a robotic arm into the imaging setup, this approach enhances scanning flexibility and precision, enabling scans across the entire body of a mouse. This extension of the imaging time window allows for comprehensive assessments without the need for repeated contrast agent administrations. Additionally, the ability to simultaneously scan multiple targets within the same session significantly increases the throughput of preclinical assessments, thereby improving the efficiency and reliability of Ultrasound Molecular Imaging in clinical translation.
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Title: Sex and Architecture
Creator: Nekkanti, Hashika C.
Date: 2023
Description: This thesis delves into the fascinating and intricate connection between sexual behaviour and architecture, offering a comprehensive...
Show moreThis thesis delves into the fascinating and intricate connection between sexual behaviour and architecture, offering a comprehensive exploration of the multifaceted factors that shape human sexuality within the context of built environments. The research is divided into six chapters, each providing a distinct perspective on the complex relationship between sexuality and the spaces we inhabit. Chapter 1 serves as an introduction, setting the stage for the study and highlighting the importance of understanding how architectural design and spatial arrangements can influence and be influenced by human sexual behaviours. Chapter 2, "Milieu and Sexed Bodies," delves into the impact of environmental stimuli on sexual arousal. By examining how architectural elements, aesthetics, and spatial configurations can elicit eroticism and arousal, this chapter sheds light on the subtle ways in which built environments interact with our intimate desires. Furthermore, it delves into the psychological aspects of fetishism and voyeurism, exploring how these sexual behaviours find expression within architectural settings. Chapter 3, titled "Sexual Behaviour," delves into the profound influence of history on human sexuality. It examines how cultural norms, religious beliefs, and social backgrounds have shaped and continue to shape sexual attitudes and behaviours across different societies and time periods. The chapter also explores the concept of polymorphous behaviour, emphasizing how architecture can create spaces that cater to diverse expressions of human sexuality. Additionally, it investigates the impact of queer spaces, highlighting the significance of inclusive design in fostering a sense of belonging and acceptance for individuals with diverse sexual identities. Chapter 4 turns its attention to "Mediated Sexuality," offering a historical analysis of how various forms of media have played a pivotal role in shaping sexual attitudes and behaviours. From ancient art to contemporary pornography, this chapter explores how media representations have influenced perceptions of sexuality, and it examines the emergence of pornomodernism, a cultural phenomenon impacting both media and architectural expressions of eroticism. Moreover, it investigates how architecture has incorporated and responded to the eroticized spaces depicted in media. Chapter 5 focuses on the "Coital Environment," a fascinating aspect of architecture that intertwines with sexual behaviour. This chapter delves into the realm of sex tourism, examining how certain destinations and spaces have become associated with sexual encounters. It analyses the design and function of dedicated places for sex within architectural contexts, providing insights into the factors that influence the creation and acceptance of such spaces in different societies. Finally, Chapter 6 presents a comprehensive "Conclusion," synthesizing the key findings from the preceding chapters. It emphasizes the critical role that architecture plays in shaping human sexual behaviours and highlights the social and cultural implications of design decisions in built environments. The chapter concludes with reflections on the significance of creating inclusive and supportive spaces that celebrate and embrace diverse sexual identities and experiences, paving the way for more empathetic and human-centric architectural design in the future. In conclusion, this thesis offers a profound exploration of sexual behaviour and architecture, shedding light on the intricate interplay of environmental stimuli, historical influences, and mediated sexuality in shaping our intimate experiences within the spaces we inhabit. It serves as a valuable resource for architects, urban planners, social scientists, and anyone interested in creating environments that foster a positive and inclusive approach to human sexuality.
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Title: Efficacy and Mechanisms of Power Ultrasound-Based Hurdle Technology for Reduction of Pathogens in Fresh Produce
Creator: Zhou, Xinyi
Date: 2023
Description: Minimally processed produce is frequently contaminated with foodborne bacterial pathogens. Power ultrasound is a non-thermal and cost...
Show moreMinimally processed produce is frequently contaminated with foodborne bacterial pathogens. Power ultrasound is a non-thermal and cost-effective technology that can be combined with other chemical sanitization methods. This study investigated the reduction of Listeria monocytogenes and Salmonella Newport on grape tomato, romaine lettuce, and spinach washed with water, chlorine, or peroxyacetic acid alone or in combination with 25 or 40 kHz power ultrasound for 1, 2, or 5 min. Produce items were inoculated with selected pathogens at approximately 10 log CFU/g, air dried for 2 h, and then treated. Combined treatment of ultrasound and sanitizers resulted in 1.44-3.99 log CFU/g reduction of L. monocytogenes and 1.35-3.62 log CFU/g reduction of S. Newport on washed produce items, with significantly higher reductions observed on grape tomato. Synergistic effects were achieved with the combined treatment of power ultrasound coupled with the chemical sanitizers when compared to the single treatments. An additional 0.48-1.40 log CFU/g reduction of S. Newport was obtained with the combined treatment on grape tomato. In general, no significant differences (p<0.05) were observed in pathogen reductions between the selected ultrasound frequencies, sanitizers, or treatment lengths. Results from this study suggest that incorporation of power ultrasound to current treatment can enhance bacterial pathogen reduction on fresh produce surface, but cannot completely eliminate bacterial pathogens. Transcriptomic study revealed significant (|Log2 fold change|<1 and false discovery rate < 0.05) transcriptional changes in L. monocytogenes LS810 in response to the 2 min power ultrasound treatment. The up-regulation of genes encoding TPI, LLO, and PTS indicates increased energy requirements, enhanced virulence, and demand for sugar sources in bacteria. On the other hand, the down-regulation of genes involved in cyclic dimeric GMP hydrolysis and transcriptional regulation suggests a modulation of intracellular signaling, cellular processes, and metabolisms to enhance survival and recovery. The GO and KEGG analysis demonstrated defense mechanisms against ultrasound stress more comprehensively. L. monocytogenes adjusts its metabolism, repairs cell membranes, and conserves energy for survival. These findings enhance our understanding of its adaptation to environmental stress. Results of this study can be used as a start point for optimizing the efficacy of ultrasound-based hurdle treatments for fresh produce disinfection.
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Title: Development of Granular Jamming Soft Robots from Boundary Constrained to Interconnected Systems
Creator: Tanaka, Koki
Date: 2023
Description: This dissertation provides a detailed study on the conceptualization, creation, and optimization of a unique, interconnected soft robot system...
Show moreThis dissertation provides a detailed study on the conceptualization, creation, and optimization of a unique, interconnected soft robot system. It introduces a flexible assembly of locomotive robotic modules interconnected by an envelope, capable of granular jamming. In doing so, it highlights the practical capabilities of these interconnected modules to adapt and function cohesively as a single robot system.As a precursor to the primary investigation, the study initially presents the development and experimental validation of a boundary constrained mobile soft robot. This design leverages granular jamming for locomotion and object grasping, thereby laying a robust foundation for the subsequent exploration of complex soft robotic systems.The cornerstone of this study is the development of an interconnected soft robot system, where locomotive robotic modules, primarily composed of an elastic material, are bound together by a flexible envelope designed for granular jamming. The robotic modules, fundamentally constructed from an elastic material, incorporate origami-inspired artificial muscle actuators. These actuators, with their semi-soft characteristics, complement the inherent flexibility of the modules and play a significant role in facilitating module propulsion. Although the design incorporates a traditional rigid power source, as opposed to a fully soft robot system, the integration of a pneumatic power method into the system successfully reduces the mechanical intricacy and unwieldiness typically associated with rigid mechanisms.This research further probes into the diverse applications of this interconnected soft robot system. Its ability to shape-shift and maintain these forms during locomotion exemplifies a robust control strategy for the system that may undergo substantial deformation, proving instrumental in dynamic environments. The study demonstrates a methodology for object manipulation and obstacle avoidance that does not rely heavily on precise control and sensing. Instead, it utilizes the inherent compliance of the soft robot system. In a notable departure from previous studies, the system also exhibits a unique capability for ascending and traversing inclined surfaces.Additionally, the study dives into the optimization of the interconnected robot system via a physics-based simulation and genetic algorithm. This approach results in an assortment of optimized configurations that excel in object grasping tasks of various shapes, thereby laying a robust groundwork for the progression of soft robotics in the future.In conclusion, this investigation reveals groundbreaking insights into the field of soft robotics through the successful design and optimization of an interconnected soft robot system. Its standout performances in deformation, manipulation, and navigation tasks set it apart. This work serves to significantly enhance the adaptability and functionality of future robotic systems, pushing the edge of what is possible across a diverse range of sectors. By portraying a significant step towards a future where robots can dynamically adapt to their environments and efficiently accomplish complex tasks, this dissertation exemplifies a transformative stride in the field.
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Title: Evaluation of Bridge Abutment Slope Protection at Stream Crossings
Creator: Wang, Peng
Date: 2023
Description: Extensive research has revealed that scour and flooding contribute to over 50% of bridge failures in the United States, with scour-induced...
Show moreExtensive research has revealed that scour and flooding contribute to over 50% of bridge failures in the United States, with scour-induced failures alone causing the collapse of 20-100 over-water bridges annually out of a total population of approximately 504,000 bridges. Within Wisconsin, a significant number of bridges, specifically over 1200, have been identified as scour-critical, with 200 of them experiencing slope instability issues.This study focuses on the problematic bridge sites in Wisconsin, particularly examining the underperformance of abutment slopes. To identify and document these problematic bridges, a comprehensive survey was conducted, followed by site visits. Subsequently, a thorough Limit Equilibrium Method (LEM) simulation was carried out based on an investigated bridge. The simulation results indicate that the infiltration of water into the slope berm areas significantly decreases slope stability due to seepage forces. Furthermore, the absence of riprap toe protection can result in overall slope failure. The implementation of concrete pouring to address riprap scoring has proven unreliable, leading to frequent failures.Additionally, simulations were performed for grouted riprap, slope walls, grouted tiebacks, and piles. The results demonstrate their potential to enhance slope safety, with their suitability requiring careful evaluation. Notably, a simulation comparing a 1:2 slope design with a 1:1.5 slope inclination reveals that the former significantly improves slope safety.In Chapter 5, a comprehensive life cycle cost analysis is conducted, comparing the 1:2 slope design to the 1:1.5 design. The analysis reveals that the 1:2 design method is more cost-effective over a 60-year study period.In conclusion, this research provides valuable insights into the assessment and mitigation of abutment slope protection issues in Wisconsin. The findings emphasize the importance of considering seepage forces, appropriate riprap installation, and alternative stabilization measures together with a comprehensive life cycle cost analysis. The research contributes to enhancing slope safety and informs decision-making processes for bridge design and maintenance.
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Title: Certified Rehabilitation Counselors' Knowledge, Stigma, and Self-Efficacy in Working with Non-Suicidal Self-Injury
Creator: Tseng, Yen Chun
Date: 2023
Description: Certified Rehabilitation Counselors (CRCs) are professionals who are responsible for supporting the rights and independence of people with...
Show moreCertified Rehabilitation Counselors (CRCs) are professionals who are responsible for supporting the rights and independence of people with disabilities. They provide services such as mental health counseling, vocational counseling, advocacy, and psychoeducation to people with disabilities. Suicide prevention and safety education are within the scope of services provided by CRCs as well. Non-suicidal self-injury (NSSI), one of the strongest risk factors for suicide attempts (Franklin et al., 2017; Kiekens et al., 2018), has received more attention as people with disabilities have elevated risk to engage in such behaviors (Coduti et al., 2016). NSSI refers to the socially unacceptable behavior causing intentional and direct injury to one’s own body tissue without conscious suicidal intent (Nock & Favazza, 2009). As the prevalence of NSSI increases, it is likely that in their professional tenure, CRCs will interact with clients who have engaged in NSSI. It is within CRCs scope of practice to advocate at individual, group, institutional, and societal levels to promote opportunity and access, improve quality of life for individuals with disabilities (Commission on Rehabilitation Counselor Certification, [CRCC], 2023). However, few studies have explored CRCs’ training, stigma, and self- efficacy when working with NSSI. The purpose of this study was to explore the nature and extent of NSSI training received by CRCs, CRCs’ stigma towards individuals engaging in NSSI, and factors associated with CRCs’ self-efficacy for working with clients with NSSI. CRCs practicing in the United States participated in the study (N = 91). Less than half of the participants reported that they received NSSI training in the past. In addition, they demonstrated some knowledge of NSSI while holding some misconceptions of NSSI at the same time. In addition, CRCs reported generally positive attitudes toward NSSI. Predictors examined in the study included training, knowledge, familiarity, and attitudes toward individuals engaged in NSSI while controlling for participants’ age and gender. Hierarchical regression analysis was used to analyze whether these factors were associated with self-efficacy to work with clients with NSSI. Results indicated that training and stigma (helping attitude) were significant predictors of CRCs’ self-efficacy for working with clients experiencing NSSI. Additionally, the variance in self-efficacy was accounted for by NSSI training and stigma. CRCs who received NSSI training in the past reported more positive attitudes and perceived themselves as more capable to work with clients who engaged in NSSI. This study is among the few to examine specific factors impacting CRCs’ self-efficacy in working NSSI. Implications for practice and research are discussed.
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Title: First-principles study on the stability, electrochemical property, and degradation mechanism of ceramic electrode materials
Creator: Wei, Jialiang
Date: 2023
Description: First-principles studies demonstrate the capability to rapidly and accurately calculate desired properties in battery materials. This thesis...
Show moreFirst-principles studies demonstrate the capability to rapidly and accurately calculate desired properties in battery materials. This thesis focuses on the examination of layered NaCrO2 as a case study to assess the impact of various calculation methods. Additionally, a microscopic analysis is conducted to investigate the failure mode of NaCrO2. Lastly, a successful first-principles based high-throughput screening of electrode materials is performed to identify stable compounds that enable easy Li migration.The layered O3 NaCrO2 compound exhibits promising characteristics as a Na-ion cathode material, including good thermal stability and specific capacity. However, it suffers from poor rate capability. To address this limitation and develop high-rate Na-ion cathodes, we conducted a first-principles study that focused on the stability and Na diffusion in pure and doped NaCrO2. The study utilized various functionals, including those explicitly incorporating van der Waals (vdW) interactions. By including vdW interactions, we observed a significant reduction in interlayer distances within partially desodiated NaCrO2, which directly impacted the prediction of Na diffusion barriers. We established a linear relationship between interlayer distance and diffusion barrier using different functionals. Notably, the increased diffusion barriers were mainly due to the reduced interlayer distances predicted by the vdW-inclusive functionals, rather than the inclusion of vdW interactions in the transition state calculations. Other factors, such as the charge density change introduced by different dopants, also influenced the Na diffusion barriers. Metal doping (Al, Zn, Mn, and Co) at low concentrations in NaCrO2 had minor effects on its thermodynamic stability but significantly promoted Na diffusivity. Among the doped NaCrO2 compounds, Co-doped NaCrO2 exhibited the lowest Na diffusion barriers and emerged as a potential candidate for high-rate Na-ion cathode materials. This study highlights the significance of vdW interactions in layered transition metal oxides and provides strategies to enhance first-principles predictions for such structures.Then, TM migration usually occurs at highly charged states in layered Na transition metal oxide, leading to a deterioration in capacity and reversibility. Furthermore, the formation of hybrid phases, characterized by the intergrowth of octahedral and prismatic Na layers, is known to take place at highly charged states. These hybrid phases often exhibit greater stability compared to simple O3 or P3 stacking configurations. However, there is limited understanding regarding the mechanism and impact of TM migration in these hybrid phases. To address this gap, we conducted a comparative first-principles study to elucidate the connection between structural changes and Cr migration in layered O3 and hybrid-phased NaCrO2. We observed that the hybrid-phased NaCrO2 experienced more significant layer shrinkage than the O3 phase after Cr migration. Three factors were found to affect the Cr migration energy: the Na concentration, local 3D configuration, and 2D in-plane geometry. Low Na concentration and specific 3D configurations facilitated Cr migration. Furthermore, the Cr migration barriers in both O3 and hybrid-phased NaCrO2 were found to be positively correlated with Cr migration energy. Lastly, we surveyed the Cr migration of 17 doped O3 and hybrid-phased NaCrO2 compounds. A uniform distribution of Cr-O bond length usually indicated suppressed Cr migration. We identified optimal dopants for Cr migration suppression by considering both Cr and dopant migration energy. This comparative study on Cr migration in O3 and hybrid-phased NaCrO2 highlights the significant role of hybrid phases in the application of layered cathode materials.Moving from the calculations of single material system, we last conduct a first-principles high-throughput screening of multicomponent transition metal sulfides (TMS) as fast Li-ion intercalation compounds. We compared two representative TMS frameworks, pyrite and spinel, with regard to their selectivity in forming stable disordered TMS. To quantify the ability to form entropy stabilized disordered TMS, we examined the effects of cation permutation on the formation enthalpy range. Although low energy-above-hull (Ehull) is a preliminary requirement for the formation of stable TMS, a narrow formation enthalpy range can also lead to entropy stabilized TMS, as only a small amount of excess energy is required to stabilize the metastable configurations. Among the 70 pyrite and spinel frameworks studied, we selected 13 spinel compounds based on their low Ehull and narrow Ef range. Additionally, these spinel compounds exhibited greater stability compared to their pyrite counterparts. We found that early transition metal elements such as Ti and V were less favorable for the formation of pyrite TMS, while late TM elements, especially Cu, strongly destabilized spinel TMS. The spinel (CrMnCoNi)S2 TMS demonstrated the most promising characteristics with a narrow Ef range. Finally, we calculated and ranked the Li migration barriers in the 13 stable spinel TMS using a bond valence-based method, which allowed for quick screening of ion migration. High oxidation state TM elements, such as Mn4+ and Cr3+, located nearest to the Li migration path, increased the Li migration barrier. (CrMnCoNi)S2 exhibited the lowest Li migration barrier, positioning it as a promising entropy-stabilized spinel intercalation compound.
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Title: An Alternative Approach for the Jefferson Lab Electron-Ion Collider Ion Accelerator Complex
Creator: Martinez Marin, Jose Luis
Date: 2020
Description: An assessment by the National Academy of Sciences (NAS) of the scientific merit for a future Electron Ion Collider (EIC) in the US concluded...
Show moreAn assessment by the National Academy of Sciences (NAS) of the scientific merit for a future Electron Ion Collider (EIC) in the US concluded that such a facility would be unique in the world and enable indispensable research on current and compelling scientific questions. This assessment confirmed the recommendations of the 2015 Nuclear Science Advisory Committee (NSAC) for an EIC with highly polarized beams of electrons and ions, sufficient luminosity and sufficient, variable center-of-mass energy. Proposals were requested for a cost-effective design that uses existing accelerator infrastructure to reduce the risk; one of two major proposals submitted for consideration originated from the Thomas Jefferson National Accelerator Facility (JLab). The Jefferson Laboratory Electron-Ion Collider (JLEIC) would use the Continuous Electron Beam Accelerator Facility (CEBAF) at JLab as a full-energy electron injector. The primary accelerator challenges are twofold: producing and maintaining a high degree of polarization for both beams, and achieving high luminosity. This thesis project was part of an effort to produce an alternative, low-risk and cost- effective design for the JLEIC ion complex. The primary goal was not to find a replacement for the JLEIC ion complex design, but rather to investigate alternative options for the different components of the ion complex that could lower the overall cost, reduce its footprint, mitigate risk, and identify possible staging or future upgrades of the project. The platform for this thesis was the alternative design for the JLEIC ion complex that included (1) a more compact ion linac, (2) two staged ion boosters instead of one before injection to the collider ring, with a more compact and lower energy Pre-Booster ring as the first stage, and (3) the dual use of the electron storage ring (e-ring) as a second stage ion Large Booster.The alternative design was first investigated for medium energy (65-GeV center-of-mass), and was then upgraded following the National Academy of Sciences (NAS) review to higher energy (100-GeV center-of-mass). Developing a more cost-effective design and meeting all the requirements is challenging due to several constraints imposed on the alternative approach -- for example, the use of only room-temperature magnets for both ion boosters. There are also space limitations, the need to keep the shape and crossing angle of the ion Large Booster the same as the collider ring, ensuring reasonable length and aperture requirements for the magnets, and avoiding transition crossing for all the rings, which can cause beam dilution and instabilities.Development of both the Medium-Energy and the High-Energy options is presented. The Medium-Energy option consists of a 135 MeV injector linac, a 3 GeV octagonally-shaped Pre-Booster ring and a 11 GeV Large Booster. The High-Energy option consists of a 150 MeV (~ 40 MeV/u for Pb) injector linac, a 8 GeV (~ 2.04 GeV/u for Pb) non figure-8 Pre-Booster ring and a 40 GeV proton (~ 16 GeV/u for Pb) Large Booster, which would also serve as the electron storage ring (e-ring). The figure-8 shape of the Large Booster helps to maintain high polarization. High luminosity is achieved following a strategy to have a high bunch repetition rate of the colliding beams, very short bunch lengths, and small transverse emittances; the main concern here is to provide a lattice that is consistent with these requirements. The main results reported are the lattice design optimization and consolidation, benchmarking of the beam optics with different codes such as ELEGANT, COSY-Infinity, MAD-X, TRACE-3D, and Zgoubi, and spin resonance simulation results. Spin dynamics studies were performed for the linac and the Pre-Booster, and mechanisms to preserve the polarization are proposed. Beam formation and non-linear effects such as chromaticity, space charge, and intra-beam scattering were also studied to gain understanding of how the alternative approach could affect the baseline beam formation scheme and to ensure that the beam requirements are met through the injector chain with this alternative approach. It was shown that the polarization can be preserved through the alternative ion complex even with the more compact linac and a Pre-Booster that does not have a figure-8 shape by using a sufficiently long spin correction solenoid in the linac and a partial Siberian snake in the Pre-Booster. The baseline beam formation scheme could still be used to reach the required beam characteristics for collider injection. Cooling is not needed in the more compact Pre-Booster, and the large, higher energy booster helps to avoid space charge effects at extraction. This study has confirmed the effectiveness of the alternative approach as concerns the optics, acceleration, polarization, and beam formation. The ion injectors are sufficiently compact, and the ion Large Booster size and shape are consistent with the e-ring requirements, enabling the desired dual functionality of that machine. This work created a basis for design discussions during the JLEIC design process. The final High-Energy design for the JLEIC ion complex adopted design features that came from the alternative design studies, which were derived in part from this work—in particular, the shorter, lower-energy linac, the use of two boosters in the injection chain before the collider ring, and the ability to have only room-temperature magnets in the boosters, with superconducting magnets used only in for the collider ring.
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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: IMPACT OF DATA SHAPE, FIDELITY, AND INTER-OBSERVER REPRODUCIBILITY ON CARDIAC MAGNETIC RESONANCE IMAGE PIPELINES
Creator: Obioma, Blessing Ngozi
Date: 2020
Description: Artificial Intelligence (AI) holds a great promise in the healthcare. It provides a variety of advantages with its application in clinical...
Show moreArtificial Intelligence (AI) holds a great promise in the healthcare. It provides a variety of advantages with its application in clinical diagnosis, disease prediction, and treatment, with such interests intensifying in the medical image field. AI can automate various cumbersome data processing techniques in medical imaging such as segmentation of left ventricular chambers and image-based classification of diseases. However, full clinical implementation and adaptation of emerging AI-based tools face challenges due to the inherently opaque nature of such AI algorithms based on Deep Neural Networks (DNN), for which computer-trained bias is not only difficult to detect by physician users but is also difficult to safely design in software development. In this work, we examine AI application in Cardiac Magnetic Resonance (CMR) using an automated image classification task, and thereby propose an AI quality control framework design that differentially evaluates the black-box DNN via carefully prepared input data with shape and fidelity variations to probe system responses to these variations. Two variants of the Visual Geometric Graphics with 19 neural layers (VGG19) was used for classification, with a total of 60,000 CMR images. Findings from this work provides insights on the importance of quality training data preparation and demonstrates the importance of data shape variability. It also provides gateway for computation performance optimization in training and validation time.
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Title: LOW-COVERAGE GENOMES AS AN EFFECTIVE AND ECONOMICAL APPROACH FOR LEPIDOPTERAN MICROSATELLITE ISOLATION
Creator: Liang, Huijia
Date: 2020
Description: This study aimed to verify that whether a low-coverage genome can work as an effective approach to isolate Lepidopteran microsatellites. As...
Show moreThis study aimed to verify that whether a low-coverage genome can work as an effective approach to isolate Lepidopteran microsatellites. As microsatellites are useful tool to study population genetics, and there are many Lepidopteran agriculture pests which can cause huge economic damages every year, additionally, Lepidoptera have abundant similar flanking sequences making it difficult to develop reliable microsatellites. However, there are not enough published genomes of Lepidoptera species. If low-coverage Lepidopteran genomes can be used to isolate reliable microsatellites, the low-coverage genomes would be an effective and economical approach for microsatellites isolation, because low-coverage genome sequencing is much cheaper and less time-consuming than the published genome sequencing.
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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

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