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Full-Text Articles in Entire DC Network
Terpene Bioproduction From Non-Model Yeast: Omics Analysis And Metabolic Modeling For Guiding Scaleup Optimization, Alyssa Worland
Terpene Bioproduction From Non-Model Yeast: Omics Analysis And Metabolic Modeling For Guiding Scaleup Optimization, Alyssa Worland
McKelvey School of Engineering Graduate Student Theses & Dissertations
Sustainability efforts have driven significant advancements in synthetic biology, particularly through the development of microbial cell factories designed for waste reduction and resource conservation. This dissertation seeks to characterize a microbial biorefinery platform for the biosynthesis of terpene compounds from yeast, with an emphasis on the industrial bioconversion of waste lipids. Terpene compounds play crucial roles in various industrial applications; however, traditional methods of terpene production have sustainability and productivity challenges that could be overcome by using microbial biosynthesis. The yeast Yarrowia lipolytica is a microbial host well suited for converting waste oils into value-added terpenes due to its native …
The Encoding Of Decision Variables In Orbitofrontal Cortex (Ofc) Is Longitudinally Stable And Varies By Cortical Layer, Manning Zhang
The Encoding Of Decision Variables In Orbitofrontal Cortex (Ofc) Is Longitudinally Stable And Varies By Cortical Layer, Manning Zhang
McKelvey School of Engineering Graduate Student Theses & Dissertations
Economic choices entail computing the values of different options and then making choice by comparing values. Work in primates and rodents has shown that these mental processes rely on the OFC. Neurophysiology studies identified in OFC distinct groups of neurons encoding the value of individual options, the binary choice outcome, and the chosen value. These variables capture both the input and the output of the decision process, suggesting a decision circuit existing in OFC. A primary challenge for the field is to assess the structure and mechanisms governing this circuit. A first fundamental question is whether the circuit is stable …
Reimagining The Machine Vision Pipeline In Cyber Physical Systems For Trustworthiness And Efficiency, Adith Boloor
Reimagining The Machine Vision Pipeline In Cyber Physical Systems For Trustworthiness And Efficiency, Adith Boloor
McKelvey School of Engineering Graduate Student Theses & Dissertations
Cyber-physical systems (CPS), including autonomous vehicles, drones, and mobile robots, rely on intricate sensors, actuators, and machine learning algorithms to perceive the physical world and execute actions within their surroundings. In the context of vision-driven CPS, achieving this demands processing a substantial volume of visual data captured by on-board cameras. The data is subsequently channeled through digital processors and harnessed by deep neural networks for tasks such as image classification, object detection, and depth perception. This data-centric, machine-vision-infused CPS fosters intelligent decision-making, thereby enhancing overall system performance. Trustworthiness, encompassing the robustness of the entire machine-vision pipeline, and system-level efficiency are …
Quantitative Approaches To Dissect Bivalent Antibody Binding And Detect Viruses From Aerosolized Samples, Ananya Benegal
Quantitative Approaches To Dissect Bivalent Antibody Binding And Detect Viruses From Aerosolized Samples, Ananya Benegal
McKelvey School of Engineering Graduate Student Theses & Dissertations
Influenza A virus (IAV) poses substantial epidemiological burdens around the world, with an estimated annual global mortality rate in the hundreds of thousands. Its rapid rate of mutation gives it a propensity for causing seasonal epidemics and occasional pandemics. As an airborne virus, IAV is most commonly transmitted through droplets and aerosols. Antibodies play a crucial role in the immune defense against IAV infection. By understanding the mechanisms of antibody-mediated defense and the transmission dynamics of IAV, we can better inform strategies for prevention, vaccination, and treatment, ultimately mitigating its impact on public health. The work encompassed in this dissertation …
Developing Naturalistic Precision Functional Mapping For High-Density Diffuse Optical Tomography, Aahana Bajracharya
Developing Naturalistic Precision Functional Mapping For High-Density Diffuse Optical Tomography, Aahana Bajracharya
McKelvey School of Engineering Graduate Student Theses & Dissertations
Advancements in non-invasive imaging have enabled extensive research into higher-order cognitive functions of the brain. Functional Magnetic Resonance Imaging (fMRI) has provided valuable insights into brain networks underlying various cognitive processes. However, limitations such as confined environments and scanner noise pose challenges for fMRI to be broadly applicable across all demographics and experimental conditions, especially in speech and language studies. Because of this, there is a need for complementary techniques that can help understand the brain as it functions during everyday scenarios. High Density Diffuse Optical Tomography (HD-DOT) is an emerging functional near-infrared spectroscopy-based technique with comparative advantages over fMRI, …
Discrete Element Method For Mining Industrial Applications: Solving The Clumping Problem Caused By Bulk Cohesive Particles In An Iron Ore Beneficiation Process, Shuang Liu
McKelvey School of Engineering Graduate Student Theses & Dissertations
The discrete element method (DEM) is a widely used numerical approach for simulating and analyzing the behavior of granular materials in various applications. This research focuses on the iron ore beneficiation process, addressing the clumping issue in cohesive iron ores from existing crushing processes through a novel double-layered disperser design. The significance of this study lies in its potential to enhance the efficiency of the existing crushing phase and improve the linkage to subsequent purification stages that target smaller-sized iron ore pellets, thereby enhancing the overall efficiency of the ore beneficiation process and achieving significant energy savings. This research adopts …
Integrating Physics And Deep Learning For Transmission-Less Attenuation Compensation In Clinical Spect, Zitong Yu
McKelvey School of Engineering Graduate Student Theses & Dissertations
Attenuation compensation (AC) is beneficial for visual interpretation and serves as a prerequisite for quantification tasks in single-photon emission computed tomography (SPECT) imaging. However, conventional AC methods typically rely on a separate X-ray CT component, leading to multiple challenges. In this context, studies have shown that scatter-window projection data contains information to estimate the attenuation distribution. Furthermore, large amounts of SPECT emission data in both photopeak and scatter-energy windows and corresponding CT scans are available. The ability of deep learning (DL) to model complex relationships by leveraging large datasets motivates its use for transmission-less AC in SPECT. Building upon the …
Investigating Catalytic Conversion Of Lignin To Valuable Products, Jialiang Zhang
Investigating Catalytic Conversion Of Lignin To Valuable Products, Jialiang Zhang
McKelvey School of Engineering Graduate Student Theses & Dissertations
Lignin is a complex, random, and heterogeneous biopolymer in lignocellulosic biomass. It has significant potential for conversion into valuable chemicals and fuels. However, its natural recalcitrant structure has made selective depolymerization challenging. This dissertation presents a detailed investigation into the mechanisms of lignin disassembly and structural evolution under various catalytic and solvent conditions. The research spans three key studies. In Chapter 2, operando magic-angle spinning (MAS) solid-state nuclear magnetic resonance (NMR) spectroscopy was employed to study reaction pathways and kinetics of lignin model polymers during catalytic hydrogenolysis. We used a Ni-Al2O3 catalyst in methanol under high temperature and pressure, and …
Terpene Bioproduction From Non-Model Yeast: Omics Analysis And Metabolic Modeling For Guiding Scaleup Optimization, Alyssa Worland
Terpene Bioproduction From Non-Model Yeast: Omics Analysis And Metabolic Modeling For Guiding Scaleup Optimization, Alyssa Worland
McKelvey School of Engineering Graduate Student Theses & Dissertations
Sustainability efforts have driven significant advancements in synthetic biology, particularly through the development of microbial cell factories designed for waste reduction and resource conservation. This dissertation seeks to characterize a microbial biorefinery platform for the biosynthesis of terpene compounds from yeast, with an emphasis on the industrial bioconversion of waste lipids. Terpene compounds play crucial roles in various industrial applications; however, traditional methods of terpene production have sustainability and productivity challenges that could be overcome by using microbial biosynthesis. The yeast Yarrowia lipolytica is a microbial host well suited for converting waste oils into value-added terpenes due to its native …
Reimagining The Machine Vision Pipeline In Cyber Physical Systems For Trustworthiness And Efficiency, Adith Boloor
Reimagining The Machine Vision Pipeline In Cyber Physical Systems For Trustworthiness And Efficiency, Adith Boloor
McKelvey School of Engineering Graduate Student Theses & Dissertations
Cyber-physical systems (CPS), including autonomous vehicles, drones, and mobile robots, rely on intricate sensors, actuators, and machine learning algorithms to perceive the physical world and execute actions within their surroundings. In the context of vision-driven CPS, achieving this demands processing a substantial volume of visual data captured by on-board cameras. The data is subsequently channeled through digital processors and harnessed by deep neural networks for tasks such as image classification, object detection, and depth perception. This data-centric, machine-vision-infused CPS fosters intelligent decision-making, thereby enhancing overall system performance. Trustworthiness, encompassing the robustness of the entire machine-vision pipeline, and system-level efficiency are …
The Encoding Of Decision Variables In Orbitofrontal Cortex (Ofc) Is Longitudinally Stable And Varies By Cortical Layer, Manning Zhang
The Encoding Of Decision Variables In Orbitofrontal Cortex (Ofc) Is Longitudinally Stable And Varies By Cortical Layer, Manning Zhang
McKelvey School of Engineering Graduate Student Theses & Dissertations
Economic choices entail computing the values of different options and then making choice by comparing values. Work in primates and rodents has shown that these mental processes rely on the OFC. Neurophysiology studies identified in OFC distinct groups of neurons encoding the value of individual options, the binary choice outcome, and the chosen value. These variables capture both the input and the output of the decision process, suggesting a decision circuit existing in OFC. A primary challenge for the field is to assess the structure and mechanisms governing this circuit. A first fundamental question is whether the circuit is stable …
Spatial Insight Of Kidney Sex-Dimorphism And Tumor Evolution, Chia-Kuei Mo
Spatial Insight Of Kidney Sex-Dimorphism And Tumor Evolution, Chia-Kuei Mo
McKelvey School of Engineering Graduate Student Theses & Dissertations
The landscape of spatial biology research has transformed drastically in recent years allowing a comprehensive understanding of cellular organization and molecular mechanisms in various biological context. This thesis presents three complementary studies that advance our understanding of spatial organization in normal tissue biology and tumor evolution, utilizing cutting-edge spatial multi-omics approaches. The first study presents a comprehensive investigation of kidney sexual dimorphism across the lifespan, integrating six distinct technological platforms: single-nucleus transcriptomics, epigenomics, Visium spatial transcriptomics, Xenium single-cell resolution spatial transcriptomics, conventional immunofluorescence imaging, and co-detection by indexing (CODEX) multiplexed protein imaging. This multi-modal approach reveals that proximal tubules exhibit …
Fail-Safe Logic Design Strategies Within Modern Fpga Architectures, Priya A. Bhakta
Fail-Safe Logic Design Strategies Within Modern Fpga Architectures, Priya A. Bhakta
Electrical and Computer Engineering ETDs
Field Programmable Gate Arrays (FPGAs) are vulnerable to radiation-induced single event upsets (SEUs) and fault injection attacks, requiring the use of redundancy techniques such as fail-safe computing. Fail-safe computing refers to computing systems that revert to a non-operational safe state when a fault occurs. This work investigates circuit-level techniques and implements fail-safe computing processes as mitigation for SEUs and fault injection attacks on FPGAs. The analysis reveals vulnerabilities that exist in FPGAs over those in application-specific integrated circuits (ASIC); thus, requiring a more elaborate network of redundant circuits and checking logic. The reconfiguration capability of FPGAs adds complexity to fail-safe …
The Occurrence And Biogeochemical Cycling Of Quaternary, Ternary And Volatile Amines In Marine Systems, Mark Fitzsimons, Ruth Airs, Yin Chen
The Occurrence And Biogeochemical Cycling Of Quaternary, Ternary And Volatile Amines In Marine Systems, Mark Fitzsimons, Ruth Airs, Yin Chen
School of Geography, Earth and Environmental Sciences
This review provides a critical assessment of knowledge regarding the occurrence and behaviour of volatile, low molecular weight amines, particularly methylamines and quaternary amines, in marine aquatic systems. It provides an up-to-date evaluation of their presence within marine ecosystems, the processes likely to control their flux across the sea-air interface, and analytical techniques associated with their measurement. Interest in the occurrence and cycling of these groups of compounds in seawater has increased within the last 10–15 years, due to their potential role in climate regulation. As such, the need for wider measurements and mechanistic studies to elucidate their role within …
Family Care And Health Behavior: A Sociocultural Perspective On Ebola Virus Disease Transmission In Sierra Leone, Abubakarr Jalloh
Family Care And Health Behavior: A Sociocultural Perspective On Ebola Virus Disease Transmission In Sierra Leone, Abubakarr Jalloh
Journal of Social, Behavioral, and Health Sciences
The 2013–2016 Ebola virus disease (EVD) outbreak in West Africa was the largest and deadliest in the four-decade history of the disease. This study examined the sociocultural context of EVD transmission during the outbreak, with a particular focus on a high-risk behavior—caring for sick relatives. Guided by a sociocultural perspective on health, it specifically explored the role of family-based caregiving practices in the transmission of EVD during an outbreak. Utilizing a qualitative collective case study, I interviewed three Ebola survivors in Makeni, Sierra Leone. Content analysis resulted in two themes: (1) family care and perceived EVD transmission and (2) how …
Revisiting Territorial Sovereignty: Origins, Legitimacy, And Modern Implications, Henan Hu
Revisiting Territorial Sovereignty: Origins, Legitimacy, And Modern Implications, Henan Hu
San Diego International Law Journal
The conventional linkage between territory and sovereignty in international law requires reevaluation, with territorial rights shifting from states to nations. Drawing on Anthony Smith’s theory of historical continuity between pre-modern ethnic communities and modern nations, this article argues that legitimate claims to territory are grounded in the historical consolidation of social, economic, and political ties by ethnic groups to specific lands. It traces the evolution of territorial rights from loosely defined ethnic living areas and fluid state boundaries to the modern conception of national territories under effective control. By distinguishing sovereignty as a construct of the state and territory as …
Evolving Uk Biology Education, Helen R. Watson
Evolving Uk Biology Education, Helen R. Watson
Peninsula Medical School
School science curriculum reform is underway in the UK. Whilst each of the four devolved nations is at a different stage in this process, it is clear we are entering an era of opportunity for positive change, where curricula can be updated to reflect our current understanding of science and to better prepare learners for further study, work, and modern life more broadly.
From Factories To Homes: A Comparative Analysis Of Adaptive Reuse In New England Industrial Buildings For Multi-Family Residential Conversion, Jeremy Weeden
Theses
The adaptive reuse of industrial buildings offers a promising path toward sustainable urban development, particularly in New England. This study investigates the feasibility and energy efficiency of converting an older, unused industrial building into a multi-family residential structure by evaluating three distinct wall assemblies that preserves the exterior brick facade: existing structural brick, a typical adapted wall assembly with interior 2x4 wood construction, and a high-efficiency adapted wall assembly with an additional interior 2x6 wood construction. Through a detailed case study analysis focusing on the building’s core and shell, this research aims to identify the most effective wall assembly for …
From Sampling To Simulating: Single-Cell Multiomics In Systems Pathophysiological Modeling, Alexandra Manchel, Michelle M. Gee, Rajanikanth Vadigepalli
From Sampling To Simulating: Single-Cell Multiomics In Systems Pathophysiological Modeling, Alexandra Manchel, Michelle M. Gee, Rajanikanth Vadigepalli
Department of Pathology, Anatomy, and Cell Biology Faculty Papers
As single-cell omics data sampling and acquisition methods have accumulated at an unprecedented rate, various data analysis pipelines have been developed for the inference of cell types, cell states and their distribution, state transitions, state trajectories, and state interactions. This presents a new opportunity in which single-cell omics data can be utilized to generate high-resolution, high-fidelity computational models. In this review, we discuss how single-cell omics data can be used to build computational models to simulate biological systems at various scales. We propose that single-cell data can be integrated with physiological information to generate organ-specific models, which can then be …
…And So It Ends In A Tie, Crystal Hou
…And So It Ends In A Tie, Crystal Hou
Theses
…and so it ends in a tie is a 2D frame-by-frame animated short film produced during the course of my 3rd year as a Master of Fine Arts student in the School of Film & Animation at Rochester Institute of Technology. The film explores themes of homosexuality, female sexuality, and the history of Japanese rope bondage through the fictionalized story of a fateful encounter between a rope-wielding martial artist and a mysterious woman who captures her attention. This paper serves as a documentation of the filmmaking process, a discussion of the ideologies and goals behind its creation, and a retrospective …
Ifrd1 Is Required For Maintenance Of Bladder Epithelial Homeostasis, Bisiayo E Fashemi, Amala K Rougeau, Arnold M Salazar, Steven J Bark, Rayvanth Chappidi, Jeffrey W Brown, Charles J Cho, Jason C Mills, Indira U Mysorekar
Ifrd1 Is Required For Maintenance Of Bladder Epithelial Homeostasis, Bisiayo E Fashemi, Amala K Rougeau, Arnold M Salazar, Steven J Bark, Rayvanth Chappidi, Jeffrey W Brown, Charles J Cho, Jason C Mills, Indira U Mysorekar
Faculty, Staff and Students Publications
The maintenance of homeostasis and rapid regeneration of the urothelium following stress are critical for bladder function. Here, we identify a key role for IFRD1 in maintaining urothelial homeostasis in a mouse model. We demonstrate that the murine bladder expresses IFRD1 at homeostasis, particularly in the urothelium, and its loss alters the global transcriptome with significant accumulation of endolysosomes and dysregulated uroplakin expression pattern. We show that IFRD1 interacts with mRNA-translation-regulating factors in human urothelial cells. Loss of Ifrd1 leads to disrupted proteostasis, enhanced endoplasmic reticulum (ER stress) with activation of the PERK arm of the unfolded protein response pathway, …
Irregular Assessment Times In Pragmatic Randomized Clinical Trials, Andrea Apter, Frances K Barg, Sanjib Basu, Alex Federman, Winifred J Hamilton, Jerry A Krishnan, Tianjing Li, Russell Localio, Christine Pindle, Daniel O Scharfstein, Justin D Smith, Kaharu Sumino
Irregular Assessment Times In Pragmatic Randomized Clinical Trials, Andrea Apter, Frances K Barg, Sanjib Basu, Alex Federman, Winifred J Hamilton, Jerry A Krishnan, Tianjing Li, Russell Localio, Christine Pindle, Daniel O Scharfstein, Justin D Smith, Kaharu Sumino
Faculty, Staff and Students Publications
Deviation from protocolized assessment times is commonplace in pragmatic randomized clinical trials. Working with a stakeholder advisory board for a Patient-Centered Outcomes Research Institute®-funded project on statistical methods for handling potential biases introduced by irregular assessment times, we identified reasons for off-schedule or missed assessments. We used the Consolidated Framework for Implementation Research 2.0 to organize our findings. We conjectured that timely completion of outcome assessments is a function of multiple determinants, only some related to participants' health status. We identified potential determinants that can be modified during the protocol design stage and can be reassessed and mitigated during trial …
Re-Indigenizing And Collaboratively Tending Urban Greenspaces, Divinity Nnenne Adewale
Re-Indigenizing And Collaboratively Tending Urban Greenspaces, Divinity Nnenne Adewale
University Honors Theses
This work details the active process of land tending with the intention of re-Indigenization in the Pacific Northwest at several Portland sites; The Native American Student Community Center, PSU Oak Savanna, and the Ridgefield National Wildlife Refuge. Land tending is an intuitive process, one rooted in love and respect for life of all forms as well as becoming the perpetual student; land tending is not a skill to be mastered, only practiced. Unlike environmental management, tending cannot be done separate from the earth, in a classroom or otherwise. Connections are what tending is built on top of: the foundation; effort …
Rna-Dependent Rna Polymerase Of Predominant Human Norovirus Forms Liquid-Liquid Phase Condensates As Viral Replication Factories, Soni Kaundal, Ramakrishnan Anish, B Vijayalakshmi Ayyar, Sreejesh Shanker, Gundeep Kaur, Sue E Crawford, Jeroen Pollet, Fabio Stossi, Mary K Estes, B V Venkataram Prasad
Rna-Dependent Rna Polymerase Of Predominant Human Norovirus Forms Liquid-Liquid Phase Condensates As Viral Replication Factories, Soni Kaundal, Ramakrishnan Anish, B Vijayalakshmi Ayyar, Sreejesh Shanker, Gundeep Kaur, Sue E Crawford, Jeroen Pollet, Fabio Stossi, Mary K Estes, B V Venkataram Prasad
Faculty, Staff and Students Publications
Many viral proteins form biomolecular condensates via liquid-liquid phase separation (LLPS) to support viral replication and evade host antiviral responses, and thus, they are potential targets for designing antivirals. In the case of nonenveloped positive-sense RNA viruses, forming such condensates for viral replication is unclear and less understood. Human noroviruses (HuNoVs) are positive-sense RNA viruses that cause epidemic and sporadic gastroenteritis worldwide. Here, we show that the RNA-dependent RNA polymerase (RdRp) of pandemic GII.4 HuNoV forms distinct condensates that exhibit all the signature properties of LLPS with sustained polymerase activity and the capability of recruiting components essential for viral replication. …
Bile Acids In Inflammatory Bowel Disease: From Pathophysiology To Treatment, Samantha H Bai, Arun Chandnani, Siyan Cao
Bile Acids In Inflammatory Bowel Disease: From Pathophysiology To Treatment, Samantha H Bai, Arun Chandnani, Siyan Cao
2020-Current year OA Pubs
Inflammatory bowel disease (IBD) is a chronic condition that affects about 7 million people worldwide, and new therapies are needed. Understanding the complex roles that bile acids (BAs) play in IBD may lead to the development of novel IBD treatments independent of direct immunosuppression. This review discusses the latest discoveries in the roles BAs play in IBD pathogenesis and explores how these discoveries offer promising new therapeutic targets to treat IBD and improve patient outcomes. Several therapies discussed include specific BA receptor (BAR) agonists, dietary therapies, supplements, probiotics, and mesenchymal stem cell therapies that have all been shown to decrease …
Womb, Gravity, And Space: Shifting Towards The Cerebellum-Basal Ganglia Paradigm In Dystonia, Diego Iacono
Womb, Gravity, And Space: Shifting Towards The Cerebellum-Basal Ganglia Paradigm In Dystonia, Diego Iacono
Department of Neurology Faculty Papers
No abstract provided.
Poems, Francis C. Macansantos
Technology And Language Learning: Exposure To Tv And Radio News And Speaking Proficiency, Taher Bahrani, Tam Shu Sim
Technology And Language Learning: Exposure To Tv And Radio News And Speaking Proficiency, Taher Bahrani, Tam Shu Sim
Kritika Kultura
Technology has dominated the world by extensive improvements in audio/visual mass media such as TV and radio. TV and radio are not just entertainment tools anymore, but can be used as pedagogically valuable technology that can provide authentic language input for language learning. This study examines the effect of exposure to TV and radio news on improving EFL learners’ speaking proficiency. To achieve this purpose, a speaking proficiency test is administered to 200 language learners, with 60 intermediate language learners selected and randomly divided into Groups 1 and 2. During the experiment, Group 1 participants are exposed to TV and …
Writing Philippine History Of Ideas And Fernando Amorsolo's Modern Art, Jovino G. Miroy
Writing Philippine History Of Ideas And Fernando Amorsolo's Modern Art, Jovino G. Miroy
Kritika Kultura
Writing Philippine history of ideas requires that we problematize the discipline of intellectual history itself. Rethinking of itself vis-a-vis cultural and social history, Philippine history of ideas would no longer rehearse the development of philosophy in the Philippines, but also of art, religion, etc. The paper discusses how Amorsolo may be considered a modern painter. Amorsolo’s art eludes comprehension because his notion of subjectivity as well as intersubjectivity transgresses the Cartesian break between subject and object. As a modern painter, he positioned himself as an individualist, but was still able to communicate to his culture.
Subaltern Planet Of Cultural Studies, Charlie Samuya Veric
Subaltern Planet Of Cultural Studies, Charlie Samuya Veric
Kritika Kultura
A contribution to a mostly unwritten history, the essay provides a preliminary account of cultural studies in Asia, Africa, and Latin America from decolonization to globalization. My intention is two-fold, namely, to contribute to the history of cultural studies in the global South and experiment with the writing of planetary history to determine the lessons that can be learned when totality is imagined from below. I argue that whether it is the geopolitics of decolonization in Asia, the politics of indigenization in Africa, or the critique of knowledge-production in Latin America, cultural studies signifies the unfinished task of decolonization.