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Causal Discovery For Relational Domains: Representation, Reasoning, And Learning, Marc Maier
Causal Discovery For Relational Domains: Representation, Reasoning, And Learning, Marc Maier
Doctoral Dissertations
Many domains are currently experiencing the growing trend to record and analyze massive, observational data sets with increasing complexity. A commonly made claim is that these data sets hold potential to transform their corresponding domains by providing previously unknown or unexpected explanations and enabling informed decision-making. However, only knowledge of the underlying causal generative process, as opposed to knowledge of associational patterns, can support such tasks. Most methods for traditional causal discovery—the development of algorithms that learn causal structure from observational data—are restricted to representations that require limiting assumptions on the form of the data. Causal discovery has almost exclusively …
Environmental Change And The Agro-Pastoralist Livelihood In The Andes Of Peru, Meagan M. Mazzarino
Environmental Change And The Agro-Pastoralist Livelihood In The Andes Of Peru, Meagan M. Mazzarino
Doctoral Dissertations
This dissertation research focuses on a high elevation Andean social-ecological system. It examines system linkages between climate, grazing pasture (wetlands), and agro-pastoralist livelihood strategies in an indigenous peasant community. Working within the conceptual framework of complex systems dynamics and sustainable livelihoods analysis, methods and concepts are synthesized from the disciplines of climatology, hydrology, remote sensing and political ecology, and results contribute to the transdisciplinary literature on vulnerability analysis within the context of environmental change. In the Andes of southern Peru livelihoods are based on agro-pastoralist activities that rely on access to natural resources in the puna ecosystem. The majority of …
Engineered Nanoparticles For Detection And Treatment Of Bacteria And Biofilms, Xiaoning Li
Engineered Nanoparticles For Detection And Treatment Of Bacteria And Biofilms, Xiaoning Li
Doctoral Dissertations
Rapid and sensitive detection and identification of bacteria woud control and prevent bacterial infection and disease, enhancing the likelihood of early diagnosis and treatment. Especially developing effective biosensor for identification of bacteria species involved in formation of biofilms, which cause chronic and persistent diseases, would promote diagnostic and therapeutic efficiency. Conventional detection methods are limited by sensitivity and required time. First part of my research has been focused on developing a rapid, simple, and sensitive biosensor aiming at portable device application for detection of bacteria in water samples. This sensor is able to detect bacteria at low concentration and generate …
Functional Nanocomposites From Self-Assembly Of Block Copolymers With Nanoparticles, Xinyu Wang
Functional Nanocomposites From Self-Assembly Of Block Copolymers With Nanoparticles, Xinyu Wang
Doctoral Dissertations
This dissertation studied the proper distribution and location control of nanoparticles (NPs) within block copolymer (BCP) templates. A facile ligand exchange reaction was introduced for the hydrophilic magnetic NPs (MNPs) that are readily dispersed in polar solvents with outstanding stability. Small molecule ligands were selected to associate strongly with particle surfaces, provide hydrophilic termini for polarity matching with polar solvents, and offer the potential for hydrogen-bonding interactions to facilitate NP incorporation into polymers. Areal ligand densities of NPs indicated a significant increase in the ligand coverage after the exchange reaction. Hydrophilic MNPs were shown to drive the self-assembly of BCPs …
Single Molecule Studies Of A Short Rna, Peker Milas
Single Molecule Studies Of A Short Rna, Peker Milas
Doctoral Dissertations
The material related with orientation of Cyanine dyes and their behavior at the ends of duplex RNA is also documented in [110]. Cyanine dyes are widely used to study the folding and structural transformations of nucleic acids using fluorescence resonance energy transfer (FRET). The extent to which FRET can be used to extract inter- and intra-molecular distances has been the subject of considerable debate in the literature; the contribution of dye and linker dynamics to the observed FRET signal is particularly troublesome. We used molecular dynamics (MD) simulations to study the dynamics of the indocarbocyanine dyes Cy3 and Cy5 attached …
Inference-Based Forensics For Extracting Information From Diverse Sources, Robert J. Walls
Inference-Based Forensics For Extracting Information From Diverse Sources, Robert J. Walls
Doctoral Dissertations
Digital forensics is tasked with the examination and extraction of evidence from a diverse set of devices and information sources. While digital forensics has long been synonymous with file recovery, this label no longer adequately describes the science’s role in modern investigations. Spurred by evolving technologies and online crime, law enforcement is shifting the focus of digital forensics from its traditional role in the final stages of an investigation to assisting investigators in the earliest phases — often before a suspect has been identified and a warrant served. Investigators need new forensic techniques to investigate online crimes, such as child …
Flexible Tethers In Multi-Chromophoric Systems: Linking Photophysics With Assembly, Jeffrey M. Lucas
Flexible Tethers In Multi-Chromophoric Systems: Linking Photophysics With Assembly, Jeffrey M. Lucas
Doctoral Dissertations
Aggregation and folding events in conjugated polymers have a dramatic effect on the photophysics, and in turn, the efficiency of said species in organic electronic devices. The factors that lead to twisting, bending and folding in conjugated polymers have been studied in numerous polymeric materials, but due to the variability of these events, they remain poorly understood. To probe the spectroscopic signatures of folding and to link them with conformational and morphological features formed by these species in the solid state, a series of alternating co-polymers were then synthesized, incorporating the 2- and 4-carbon tethers with oligo-phenylenevinylene derivatives. Static absorption, …
Efficient Routing And Scheduling In Wireless Networks, Anand Seetharam
Efficient Routing And Scheduling In Wireless Networks, Anand Seetharam
Doctoral Dissertations
The temporal and spatial variation in wireless channel conditions, node mobility make it challenging to design protocols for wireless networks. In this thesis, we design efficient routing and scheduling algorithms which adapt to changing network conditions caused by varying link quality or node mobility to improve user-level performance. We design and analyze routing protocols for static, mobile and heterogeneous wireless networks. We analyze the performance of opportunistic and cooperative forwarding in static mesh networks showing that opportunism outperforms cooperation; we identify interference as the main cause for mitigating the potential gains achievable with cooperative forwarding. For mobile networks, we quantitatively …
Introducing The Newton-Poisson-Brillouin Model In The Quest For Plasmons In Metallic Carbon Nanotubes, Richard P. Zannoni
Introducing The Newton-Poisson-Brillouin Model In The Quest For Plasmons In Metallic Carbon Nanotubes, Richard P. Zannoni
Doctoral Dissertations
A new method is presented to model carbon nanotubes (CNT) of micron length. The Newton-Poisson-Brillouin (NPB) model uses Newtonian physics to model the interaction of a population of thermally excited quasi-particles. The NPB model is self-consistent with Poisson’s equation, and the quasi-particles are confined to the CNT’s band structure. In this work, we explore the parameter space of the model.
Engineering Surface Functionality Of Nanoparticles For Biological Applications, Yi-Cheun Yeh
Engineering Surface Functionality Of Nanoparticles For Biological Applications, Yi-Cheun Yeh
Doctoral Dissertations
Engineering the surface functionality of nanomaterials is the key to investigate the interactions between nanomaterials and biomolecules for potent biological applications such as therapy, imaging and diagnostics. My research has been orientted to engineer both of the surface monolayers and core materials to fabricate surface-functionalized nanomaterials through the synergistic multidisciplinary approach that combine organic chemistry, materials science and biology. This thesis illustrates the design and synthesis of the surface-funcitonalized quantum dots (QDs) and gold nanoparticles (AuNPs) for the fundamental studies and practical applications. For QDs, A new class of cationic QDs with quaternary ammonium derivatives was synthesized to provide permanent …
Patterning And Mechanical Analysis Of Fiber-Based Materials, Samuel A. Pendergraph
Patterning And Mechanical Analysis Of Fiber-Based Materials, Samuel A. Pendergraph
Doctoral Dissertations
The ability to define and control the topography of a surface has been studied extensively due to its importance in a wide variety of applications. The control of a non-planar topography would be very valuable since a number of structures that are pervasive in artificial applications (e.g. fibers, lenses) are curved interfaces. This potential of enabling applications that incorporate non-planar geometries was the motivation for this thesis. The first study of this thesis comprises the study of patterning the circumference of micrometer sized fibers. Specifically, a unique technique was described to pattern the fiber with a periodic array of colloids. …
Measurement Of The Parity Violating Asymmetry In Elastic Electron Scattering Off 208pb, Jonathan W. Wexler
Measurement Of The Parity Violating Asymmetry In Elastic Electron Scattering Off 208pb, Jonathan W. Wexler
Doctoral Dissertations
The Lead Radius Experiment (PREX) was carried out in order to provide a model independent measurement of the RMS radius √ < r2 >of the neutron distribution in the 208Pb nucleus. The parity-violating scattering asymmetry for longitudinally polarized 1.06 GeV electrons from an unpolarized 208Pb target was measured at Q2 = 0.00880 GeV2. This measurement was performed by the PREX collaboration in Hall A at Jefferson Laboratory in Newport News, VA, between March and June, 2010. The electron detectors used in this measurement were designed and fabricated by University of Massachusetts-Amherst and Smith College. The resulting …
The Discovery And Study Of Fluvirucin B1 Polyketide Synthase, Tsung-Yi Lin
The Discovery And Study Of Fluvirucin B1 Polyketide Synthase, Tsung-Yi Lin
Doctoral Dissertations
Rapidly decreasing numbers of viable therapeutic leads in the pharmaceutical pipeline demand new, sustainable methods for improved drug discovery and development. Despite vast improvements in de novo drug design and target recognition, Nature remains the richest source of small molecule therapeutics. Among many natural products, polyketides are not only the most promising ones for developing new antibiotic leads, but also exhibit unusually high therapeutic value ranging from clinical use as anticancer, antiviral, and immunosuppressant drugs. Modular polyketide synthases (PKSs) are dedicated nano-machinery that can be manipulated to produce a structurally diverse library for drug discovery programs. The ability to manipulate …
Using Formal Methods To Verify Transactional Abstract Concurrency Control, Trek S. Palmer
Using Formal Methods To Verify Transactional Abstract Concurrency Control, Trek S. Palmer
Doctoral Dissertations
Concurrent application design and implementation is more important than ever in today's multi-core processor world. Transactional Memory (TM) Concurrent application design and implementation is more important than ever in today's multi-core processor world. Transactional Memory (TM). Each has its own particular advantages and disadvantages. However, these techniques each need some extra information to `glue' the non-transactional operation into a transactional context. At the most general level, non-transactional code must be decorated in such a way that the TM run-time can determine how those non-transactional operations commute with one another, and how to `undo' the non-transactional operations in case the run-time …
Understanding Structure-Property Relationships At The Nano-Bio Interface For Delivery Applications, Krishnendu Saha
Understanding Structure-Property Relationships At The Nano-Bio Interface For Delivery Applications, Krishnendu Saha
Doctoral Dissertations
The surface chemistry of the nanomaterials creates an effective interface between two entirely different worlds: nanotechnology and biology. Understanding the interaction between nanomaterial surface chemistry and biological entities can be useful for a wide variety of biomedical applications as well as can provide crucial information for nanotoxicology. In my research, I have used gold nanoparticles as a model platform to synthesize a family of nanoparticles with atomic level control of their surface properties and probe their interaction with biological systems. First part of my research focused on the understanding the uptake mechanisms, toxicity, and hemolytic properties of cationic nanoparticles, an …
Privacy-Preserving Sanitization In Data Sharing, Wentian Lu
Privacy-Preserving Sanitization In Data Sharing, Wentian Lu
Doctoral Dissertations
In the era of big data, the prospect of analyzing, monitoring and investigating all sources of data starts to stand out in every aspect of our life. The benefit of such practices becomes concrete only when analysts or investigators have the information shared from data owners. However, privacy is one of the main barriers that disrupt the sharing behavior, due to the fear of disclosing sensitive information. This dissertation describes data sanitization methods that disguise the sensitive information before sharing a dataset and our criteria are always protecting privacy while preserving utility as much as possible. In particular, we provide …
On The Formation And Evolution Of Early-Type Galaxies, Christina Williams
On The Formation And Evolution Of Early-Type Galaxies, Christina Williams
Doctoral Dissertations
Galaxies in the local Universe are characterized by blue, star-forming disk galaxies, and red, massive early-type galaxies (ETGs) whose star-formation has been quenched early in the Universe's history. The ETGs are relics of the evolutionary processes that transform galaxies over cosmic time, but currently we still lack a comprehensive understanding of their evolution. An important link in the evolution of ETGs is that the first quenched galaxies (z~2) are both the most massive, and most compact, suggesting a physical connection between high stellar density and efficient, rapid cessation of star-formation. In this dissertation, I seek insight into the formation and …
Computational Communication Intelligence: Exploring Linguistic Manifestation And Social Dynamics In Online Communication, Xiaoxi Xu
Doctoral Dissertations
We now live in an age of online communication. As social media becomes an integral part of our life, online communication becomes an essential life skill. In this dissertation, we aim to understand how people effectively communicate online. We research components of success in online communication and present scientific methods to study the skill of effective communication. This research advances the state of art in machine learning and communication studies. For communication studies, we pioneer the study of a communication phenomenon we call Communication Intelligence in online interactions. We create a theory about communication intelligence that measures participants’ ten high-order …
Retrieval Models Based On Linguistic Features Of Verbose Queries, Jae Hyun Park
Retrieval Models Based On Linguistic Features Of Verbose Queries, Jae Hyun Park
Doctoral Dissertations
Natural language expressions are more familiar to users than choosing keywords for queries. Given that, people can use natural language expressions to represent their sophisticated information needs. Instead of listing keywords, verbose queries are expressed in a grammatically well-formed phrase or sentence in which terms are used together to represent the more specific meanings of a concept, and the relationships of these concepts are expressed by function words. The goal of this thesis is to investigate methods of using the semantic and syntactic features of natural language queries to maximize the effectiveness of search. For this purpose, we propose the …
Guanidinium-Rich Romp Polymers Drive Phase, Charge, And Curvature-Specific Interactions With Phospholipid Membranes, Michael T W Lis
Guanidinium-Rich Romp Polymers Drive Phase, Charge, And Curvature-Specific Interactions With Phospholipid Membranes, Michael T W Lis
Doctoral Dissertations
Protein transduction domains (PTDs) and their and their synthetic mimics are short sequences capable of unusually high uptake in cells. Several varieties of these molecules, including the arginine-rich Tat peptide from HIV, have been extensively used as vectors for protein, DNA, and siRNA delivery into cells. Despite the wide-ranging utility of PTDs and their mimics, their uptake mechanism is still under considerable debate. How the molecules are able to cross phospholipid membranes, and what structural components are necessary for optimal activity are poorly understood. This thesis explores how PTDMs interact with phospholipid membrane phase, anionic lipid content and negative Gaussian …
Designing Efficient And Accurate Behavior-Aware Mobile Systems, Abhinav Parate
Designing Efficient And Accurate Behavior-Aware Mobile Systems, Abhinav Parate
Doctoral Dissertations
The proliferation of sensors on smartphones, tablets and wearables has led to a plethora of behavior classification algorithms designed to sense various aspects of individual user's behavior such as daily habits, activity, physiology, mobility, sleep, emotional and social contexts. This ability to sense and understand behaviors of mobile users will drive the next generation of mobile applications providing services based on the users' behavioral patterns. In this thesis, we investigate ways in which we can enhance and utilize the understanding of user behaviors in such applications. In particular, we focus on identifying the key challenges in the following three aspects …
Mass Spectrometry Based Experimental Strategies To Characterize Native And Non-Native Disulfide Bonds In Cysteine-Rich Protein Therapeutics, Adriana Z. Kita
Mass Spectrometry Based Experimental Strategies To Characterize Native And Non-Native Disulfide Bonds In Cysteine-Rich Protein Therapeutics, Adriana Z. Kita
Doctoral Dissertations
The impact post-translational modifications (PTMs) can have on the structure, function, and immunogenicity of protein therapeutics makes it especially important for these protein-based treatments to be well characterized. Mass spectrometry has become instrumental in the examination of enzymatic and non-enzymatic PTMs. Disulfide bonds fall into both of these categories in which native disulfide bonds are formed in the ER by disulfide mediated enzymes and non-native disulfide bonds are often formed by non-enzymatic reducing/oxidizing reactions. Disulfide bonds are particularly important for protein folding and reinforcing higher order structure, and are typically characterized by LC-MS of non-reduced peptides. However, characterizing the disulfide …
Searching Based On Query Documents, Youngho Kim
Searching Based On Query Documents, Youngho Kim
Doctoral Dissertations
Searches can start with query documents where search queries are formulated based on document-level descriptions. This type of searches is more common in domain-specific search environments. For example, in patent retrieval, one major search task is finding relevant information for new (query) patents, and search queries are generated from the query patents One unique characteristic of this search is that the search process can take longer and be more comprehensive, compared to general web search. As an example, to complete a single patent retrieval task, a typical user may generate 15 queries and examine more than 100 retrieved documents. In …
Defining, Evaluating, And Improving The Process Of Verifying Patient Identifiers, Junghee Jo
Defining, Evaluating, And Improving The Process Of Verifying Patient Identifiers, Junghee Jo
Doctoral Dissertations
Patient identification errors are a major cause of medication errors. During medication administration, failure to identify patients correctly can lead to patients receiving incorrect medications, perhaps resulting in adverse drug events and even death. Most medication error studies to date have focused on reporting patient misidentification statistics from case studies, on classifying types of patient identification errors, or on evaluating the impact of technology on the patient identification process, but few have proposed specific strategies or guidelines to decrease patient identification errors. This thesis aims to improve the verification of patient identifiers (VPI) process by making three key contributions to …
Nanoparticle Building Blocks For Functional Structures, Youngdo Jeong
Nanoparticle Building Blocks For Functional Structures, Youngdo Jeong
Doctoral Dissertations
A major goal in material science is achieving a desired function using structures fabricated with designed building blocks. Advanced synthetic and self-assembly techniques allow various nanomaterials to become promising building blocks, providing the control of the interaction between building blocks. The unique properties of nanomaterials can be transferred to structured systems. Among nanomaterials, inorganic nanoparticles such as gold nanoparticles (AuNPs), magnetic particles, and quantum dots (QDs) provide useful physical properties stemming from their inorganic core, large surface areas, and oriented surface functionalities. My research has focused on fabricating functional systems using gold nanoparticles (AuNPs), manipulating the interaction between AuNPs, bio-entities, …
Factor Inhibiting Hif's (Fih) Structure Controls O2 Activation And Reactivity, John A. Hangasky Iii
Factor Inhibiting Hif's (Fih) Structure Controls O2 Activation And Reactivity, John A. Hangasky Iii
Doctoral Dissertations
Factor Inhibiting HIF (FIH) is a Fe(II)-αKG dependent oxygenase that acts as a cellular oxygen sensor in humans. FIH regulates the transcriptional activity of the hypoxia-inducible factor-1 (HIF-1a or HIF), a transcription factor responsible cellular O2 homeostasis. Hydroxylation of the target residue HIF-Asn803, found in the C-terminal transactivation domain (CTAD), inactivates HIF-dependent gene expression. Central to FIH’s function is the activation of O2 after CTAD binding. The mechanistic and structural features of FIH leading to tight coupling between CTAD binding and subsequent O2-activation and reactivity are key for efficient O2 sensing. Our mechanistic …
Investigating Fault System Deformation With Numerical Models And Analog Experiments, Justin W. Herbert
Investigating Fault System Deformation With Numerical Models And Analog Experiments, Justin W. Herbert
Doctoral Dissertations
This dissertation aims to understand fault system deformation using numerical models and analog experiments. In southern California, the southern Big Bend of the San Andreas fault (SAF) is a zone of transpression that accommodates deformation associated with the Pacific-North American plate boundary. Using three-dimensional boundary element method (BEM) models, I test the sensitivity of fault slip rates to a range of tectonic boundary conditions constrained by Global Positioning System (GPS) studies of the region (45–50 mm/yr and 320°– 325°). I have modified fault configurations derived from the Southern California Earthquake Center Community Fault Model of the San Gorgonio knot and …
Data Analysis And Study Design In The Presence Of Error-Prone Diagnostic Tests, Xiangdong Gu
Data Analysis And Study Design In The Presence Of Error-Prone Diagnostic Tests, Xiangdong Gu
Doctoral Dissertations
Interval censored time to event outcomes arise when a silent event of interest is known to have occurred within a specific time period, determined by the times of the last negative and first positive diagnostic tests. The four chapters comprising this thesis are tied together by a common theme in that the outcome of interest is an interval censored time to event random variable. In Chapter 1, we describe a stratified Weibull model appropriate for interval cen- sored outcomes and implement a new R package straweib. We compare the proposed approach with the log-linear form of the Weibull regression model …
Functional Nanoparticles At Interfaces: Emulsion Stabilization And Triggered Inversion, Caroline Laure Marie Miesch
Functional Nanoparticles At Interfaces: Emulsion Stabilization And Triggered Inversion, Caroline Laure Marie Miesch
Doctoral Dissertations
Encapsulation of materials can be performed through the stabilization of fluid-fluid interfaces and the formation of emulsion droplets, which is commonly achieved with surfactants, including small molecules and polymers, as well as particles that are, typically, micron-scale in diameter. The worked contained in this dissertation centered on droplets that are stabilized by nanoparticles, including metallic nanoparticles and semiconductor quantum dots, which bring the conductive and fluorescent properties inherent to such nanoparticles into the droplet construction. Double emulsion droplets, both oil-in-water-in-oil (o/w/o) and water-in-oil-in-water (w/o/w) were formed using nanoparticles as the only surfactant in solution. Different types of nanoparticles were found …
Studies On The Wrinkling Of Thin Polymer Films Floating On Liquid, Kamil B. Toga
Studies On The Wrinkling Of Thin Polymer Films Floating On Liquid, Kamil B. Toga
Doctoral Dissertations
This dissertation aims to broaden our understanding on wrinkling instabilities occurring on floating polymeric sheets, and tries to establish innovative methods that exploit these patterns in studies on material behavior and interfacial phenomena. We will address three major topics in this thesis including, i) characterization of the conditions required to buckle an annular disc, ii) characterization of wrinkles occurring around a droplet/bubble placed on a membrane that is kept taut at the liquid-air interface, and iii) using wrinkling patterns as a probe to understand the interfacial behavior and dynamics of ultrathin films. The first project in this thesis is about …