Physical Sciences and Mathematics Commons^™

Reconstruction Of 3d Image For Particles By The Method Of Angular Correlations From Xfel Data, Sung Soon Kim

Theses and Dissertations

The world’s first X-ray Free Electron Laser (XFEL), the Linac Coherent Light Source (LCLS) at the Stanford Linear Accelerator Center (SLAC), is now generating X-ray pulses of unprecedented brilliance (one billion times brighter than the most powerful existing sources), and at the amazing rate of only a few femtoseconds. The first such experiments are being performed on relatively large objects such as viruses, which produce low resolution, low-noise diffraction patterns on the basis of the so called “diffraction before destruction” principle. Despite the promise of using XFEL for the determination of the structures of viruses, the results so far from …

Influence Of Ndbc Buoy Design On Sea Surface Temperature Trends In The Coastal United States, Alexander Keith Nickerson

Theses and Dissertations

The sea surface temperature (SST) record is the one of the oldest climate records, stretching back to 1662. Since that time, voluntary observing ships (VOSs) have been including these data in their ship‘s log. Due to the sparseness of VOS data, moored buoys were created to provide data at regular intervals in order to provide a more continuous record with data collection unaffected by human error. The SST sensor in National Data Buoy Center (NDBC) buoys is inside a hull and not in direct contact with the ocean. Thus, the design of the buoy may subject them to additional biases …

Structural Analysis Of Cell Signaling Complexes, Takuma Aoba

Theses and Dissertations

Bardet-Biedl syndrome (BBS) is a rare genetic disease that causes retinal degradation, obesity, kidney dysfunction, polydactyly, and other cilium-related disorders. To date, more than 20 BBS genes, whose mutants cause BBS phenotypes, have been identified, and eight of those (BBS1-2, 4-5, 7-9, and 18) are known to form the BBSome complex. Recent studies have revealed that the BBSome is closely involved in the trafficking of signaling proteins in the primary cilium. Mutations in BBS genes are highly pathogenic because trafficking in the primary cilium is not fully functional when BBS mutations impair assembly of the BBSome. However, the functional links …

Algorithms For Learning The Structure Of Monotone And Nonmonotone Sum-Product Networks, Aaron W. Dennis

Theses and Dissertations

The sum-product network (SPN) is a recently-proposed generative, probabilistic model that is guaranteed to compute any joint or any marginal probability in time linear in the size of the model. An SPN is represented as a directed, acyclic graph (DAG) of sum and product nodes, with univariate probability distributions at the leaves. It is important to learn the structure of this DAG since the set of distributions representable by an SPN is constrained by it. We present the first batch structure learning algorithm for SPNs and show its advantage over learning the parameters of an SPN with fixed architecture. We …

Control Of Matrix Metalloproteinases In A Periodontitis Model: Molecules That Trigger Or Inhibit Mmp Production, Catalina Matias Orozco

Theses and Dissertations

In periodontitis, there is a disruption in the homeostasis of the oral microbiome by peridontopathogenic bacteria. However, while bacteria is essential for periodontitis to occur, the severity, pattern and progression of the disease is not solely determined by the microbial burden, and in fact has a lot to do with the overwhelming host inflammatory response. The response can vary even in two individuals with similar periodontopathogenic profiles. The host response leads to extracellular matrix (ECM) destruction, loss of attachment, alveolar bone resorption and eventually, edentulism. The host's reaction is orchestrated by proinflammatory cytokines and chemokines and matrix metalloproteinases (MMPs). MMPs …

A Self-Organized Approach For Detecting Communities In Networks, Ben Collingsworth

Theses and Dissertations

The community structure of networks reveals hidden information about the whole network structure that cannot be discerned using other topological properties. Yet, the importance of identifying community structure in networks to many fields such as medicine, social sciences and national security, calls for better approaches for performing this identification. The prevalent community detection algorithms, such as the one proposed by Girvan and Newman, utilize a centralized approach that is unlikely to scale to very large networks and does not handle dynamic networks. Further, existing algorithms provide limited information regarding community overlap, where an individual participates in multiple communities. We propose …

Optical Method For High Magnification Imaging And Video Recording Of Live Cells At Sub-Micron Resolution, Jaime E. Romo Jr.

Theses and Dissertations

Optical microscopy, the most common technique for viewing living microorganisms, is limited in resolution by Abbe’s criterion. Recent microscopy techniques focus on circumnavigating the light diffraction limit by using different methods to obtain the topography of the sample. Systems like the AFM and SEM provide images with fields of view in the nanometer range with high resolvable detail, however these techniques are expensive, and limited in their ability to document live cells. The Dino-Lite digital microscope coupled with the Zeiss Axiovert 25 CFL microscope delivers a cost-effective method for recording live cells. Fields of view ranging from 8 microns to …

Proactive Approach For The Prevention Of Ddos Attacks In Cloud Computing Environments, Brad Alshehry

Theses and Dissertations

Contemporary security systems attempt to provide protection against distributed denial-of-service (DDoS) attacks; however, they mostly use a variety of computing and hardware resources for load distribution and request delays. As a result, ordinary users and website visitors experience timeouts, captchas, and lowspeed connections. In this paper, we propose a new multilayer system for protection against DDoS in the cloud that utilizes Threat Intelligence techniques and a proactive approach to detect traffic behavior anomalies. The first layer of the model analyzes the source IP address in the header of incoming traffic packets and the second layer analyzes the speed of requests …

Investigation Of Sparsifying Transforms In Compressed Sensing For Magnetic Resonance Imaging With Fasttestcs, Christopher Adams Baker

Theses and Dissertations

The goal of this contribution is to achieve higher reduction factors for faster Magnetic Resonance Imaging (MRI) scans with better Image Quality (IQ) by using Compressed Sensing (CS). This can be accomplished by adopting and understanding better sparsifying transforms for CS in MRI. There is a tremendous number of transforms and optional settings potentially available. Additionally, the amount of research in CS is growing, with possible duplication and difficult practical evaluation and comparison. However, no in-depth analysis of the effectiveness of different redundant sparsifying transforms on MRI images with CS has been undertaken until this work. New theoretical sparsity bounds …

Quantitative Optical Studies Of Oxidative Stress In Rodent Models Of Eye And Lung Injuries, Zahra Ghanian

Theses and Dissertations

Optical imaging techniques have emerged as essential tools for reliable assessment of organ structure, biochemistry, and metabolic function. The recognition of metabolic markers for disease diagnosis has rekindled significant interest in the development of optical methods to measure the metabolism of the organ.

The objective of my research was to employ optical imaging tools and to implement signal and image processing techniques capable of quantifying cellular metabolism for the diagnosis of diseases in human organs such as eyes and lungs. To accomplish this goal, three different tools, cryoimager, fluorescent microscope, and optical coherence tomography system were utilized to study the …

Density Estimation For Lifetime Distributions Under Semi-Parametric Random Censorship Models, Carsten Harlass

Theses and Dissertations

We derive product limit estimators of survival times and failure rates for randomly right censored data as the numerical solution of identifying Volterra integral equations by employing explicit and implicit Euler schemes. While the first approach results in some known estimators, the latter leads to a new general type of product limit estimator. Plugging in established methods to approximate the conditional probability of the censoring indicator given the observation, we introduce new semi-parametric and presmoothed Kaplan-Meier type estimators. In the case of the semi-parametric random censorship model, i.e. the latter probability belonging to some parametric family, we study the strong …

Radial Basis Functions: Biomedical Applications And Parallelization, Ke Liu

Theses and Dissertations

Radial basis function (RBF) is a real-valued function whose values depend only on the distances between an interpolation point and a set of user-specified points called centers. RBF interpolation is one of the primary methods to reconstruct functions from multi-dimensional scattered data. Its abilities to generalize arbitrary space dimensions and to provide spectral accuracy have made it particularly popular in different application areas, including but not limited to: finding numerical solutions of partial differential equations (PDEs), image processing, computer vision and graphics, deep learning and neural networks, etc.

The present thesis discusses three applications of RBF interpolation in biomedical engineering …

Corrosion Of Aluminum Current Collector In Cost Effective Rechargeable Lithium-Ion Batteries, Shengyi Li

Theses and Dissertations

Rechargeable lithium ion batteries (LIB) have been widely used as commercial energy storage systems for portable equipment, electronic devices and high power applications (e.g. electronic vehicles). One issue with the commercialized LIB is that expensive, highly toxic and flammable organic solvents are used in the electrolyte and the fabrication process of electrodes. The toxic organic based solvents increase the production cost and lead to significant safety concerns in the event of a battery overcharge or short circuit. The recent development of “green manufacturing” technology allows manufacturers to replace the organic solvents used in the cathode coating process by aqueous based …

Stage-Specific Predictive Models For Cancer Survivability, Elham Sagheb Hossein Pour

Theses and Dissertations

Survivability of cancer strongly depends on the stage of cancer. In most previous works, machine learning survivability prediction models for a particular cancer, were trained and evaluated together on all stages of the cancer. In this work, we trained and evaluated survivability prediction models for five major cancers, together on all stages and separately for every stage. We named these models joint and stage-specific models respectively. The obtained results for the cancers which we investigated reveal that, the best model to predict the survivability of the cancer for one specific stage is the model which is specifically built for that …

An Open Source Approach To Serve A Large Number Of Computer Users Using Block-Level Streaming, Max D. Torres

Theses and Dissertations

There are several options for providing a large number of computers to users for their daily tasks. A typical setup may consist of a large number of computers where each relies on an HDD consisting of the required software, sufficient RAM, a capable CPU that meets the software requirements, and a stable network connection. This thesis proposes the use of the open-source AoE protocol to stream an OS to a user computer from a central server. Since the streaming is done from a well-protected central storage, the AoE protocol is less prone to failures compared to the traditional approach based …

Using Machine Learning To Predict Student Achievement On The State Of Texas Assessment Of Academic Readiness Examination In Charter Schools, Christopher D. Gonzalez

Theses and Dissertations

The purpose of this study was to research and develop a way to use machine learning algorithms (MLAs) to predict student achievement on the State of Texas Assessment of Academic Readiness (STAAR), specifically in the charter school setting. Charter schools have the disadvantage of a constant influx in students, so providing historical student data in order to analyze trends proves difficult. This study expands on previous research done on students in secondary and post-secondary school and determining features that indicate success in these settings. The data used is from the district of IDEA Public Schools who focuses on providing education …

Chemical Forms Of Nitrogen In Runoff From Diverse Florida Watersheds, Jessica Emily Voelker

Theses and Dissertations

Watershed use along the Indian River Lagoon (IRL) on the central east coast of Florida has changed drastically during the past century, bringing with it declining water quality, eutrophication, hypoxia and fish kills. The decline of the lagoon has been directly linked to nutrient overloading; however, the sources and chemical forms of nutrients to the IRL are still not well constrained. This study was designed to determine how watershed land use impacts concentrations and fluxes of the various forms of dissolved nitrogen to the IRL. Five tributaries to the IRL were sampled monthly from July 2015 – September 2016. Storm …

The Role Of Biotic And Environmental Factors In Spatial And Temporal Variability Of Indian River Lagoon Copepod Communities, Hannah G. Kolb

Theses and Dissertations

The role of zooplankton communities as the link between phytoplankton and secondary consumers is dependent on the species make-up of the copepod community. Copepods often dominate zooplankton in numbers and biomass and are frequently the dominant grazers. Species variabilities in behavioral and morphological traits, and seasonal variances in species make-up, have the potential to alter trophic dynamics in planktonic communities. The goal of this study was to identify the driving forces behind copepod community composition and better understand the role of key species in the Northern Indian River Lagoon (N-IRL). Copepods made up 76% of the N-IRL zooplankton community and …

Exploring The Role Of Biofilms In The Transport And Establishment Of Invasive Marine Macrofoulers, Lynn Holly Sweat

Theses and Dissertations

Biofilms dominated by bacteria and diatoms universally colonize submerged surfaces and mediate larval recruitment in benthic marine systems. The ability for macrofoulers to be transported by vessels and become globally established is likely affected by cues from the biofilm organisms they encounter. This study investigates how macrofoulers respond to biofilms shaped by local geography, transport processes and relocation. Biofilm assemblages in neighboring ports were largely unique to the site at which they were developed. Bacteria were primary drivers of variations among sites, and overall bacterial richness was an order of magnitude higher than has been reported for other marine environments. …

Categorizing “Muck” In The Indian River Lagoon, Florida, Based On Chemical, Physical And Biological Characteristics, Katherine Mae Beckett

Theses and Dissertations

During the past six decades, the thickness and areal extent of muck sediments have continually increased in the Indian River Lagoon (IRL), Florida. These sediments are anoxic, store and release nutrients, and destroy natural benthic habitats. The main objective of this research was to develop guidelines that help prioritize sites for muck removal based on the following: (1) biological abundance and diversity, (2) muck thickness, and (3) the physical and chemical composition of muck. Thinner muck deposits (20-40 cm), collected during two seasons at eight locations in the lagoon and adjacent creeks, had greater variability in sediment composition and ~5 …

Soteria: A Persuasive Esecurity Assistant, Punica Bhardwaj

Theses and Dissertations

“…security is only as good as the weakest link, and people are the weakest link in the chain.” – B Schneier, 2002 Humans are often referred to as the “weakest link” in the security chain because of the poor security decisions taken by them. There can be many reasons for these decisions, such as lack of understandability of the software, lack of education, and lack of relevant information required to do that particular action. In this Thesis, we focus on the lack of relevant information required at the time of performing the action. In order to provide the user with …

Studies With Dynamic Nuclear Imaging Image Reconstruction Algorithm, Haoran Chang

Theses and Dissertations

Non-negative matrix factorization (NMF) is a useful method for those non-negative multivariate data. In nuclear imaging, NMF, which is also called factor analysis, is used to analyze the 4D image of positron emission tomography and single positron emission computed tomography. Normally, we use factor analysis of dynamic structure (FADS) for the dynamic reconstruction [1]. However, this reconstruction algorithm is extremely dependent on the initial data, which means the result may be unstable when the initial data is not good enough. There are several ways for the initializing, such as splined initialized (SIFADS) [2] and clustering initialized (CIFA) [3][4]. In this …

Gbann-V: Genetically Based Artificial Neural Network With Validation For Optimal Feature Selection And Data Mining, Eric W. Worden

Theses and Dissertations

In data mining and machine learning systems, highly predictive feature attributes help researchers and data analysts classify the problem space in the most optimal way. In this thesis paper, a feature subset selection classifier system for data mining and machine learning will be presented. This feature subset selection system will test data from the PIMA Indian Diabetes Data and the Breiman Waveform Data Set. The system collects the input features and then processes them through an evolutionary search process in order to reduce the feature space into an optimal feature set. Reducing irrelevant attributes can decrease the complexity and processing …

Discrete And Continuous Operational Calculus In Stochastic Games, Kenneth Ibe Iwezulu

Theses and Dissertations

First, we consider a class of antagonistic stochastic games between two players A and B. The game is specified in terms of two "hostile" stochastic processes representing mutual attacks upon random times exerting casualties of random magnitudes. This game is observed upon random epochs of time and the outcome of the game is not known in real time. The game ends at the time when the underlying fixed threshold of either player is crossed (referred to as the first passage time). The first passage time is then shifted to an epoch, i.e. upon one of the observation instants of time. …

The Tolerance Of Benthic Infauna To Fine-Grained Organic Rich Sediments In A Shallow Subtropical Estuary, Daniel Christopher Hope

Theses and Dissertations

Fine-grained organic-rich sediments (FGORS) from anthropogenic impacts are a growing concern for bays and estuaries around the world. This study explores the relationships between infaunal community diversity and species’ abundances with FGORS in the Indian River Lagoon and its tributaries. To examine these potential relationships, infauna were collected monthly using a Petit Ponar grab at 16 stations in the central Indian River Lagoon from October 2015 to August 2016. Abundant taxa in these sediments include polychaete worms (e.g., the polychaete Nereis succinea), molluscs (e.g., clam Parastarte triquetra), and arthropods (e.g., the tanaid Leptochelia dubia) with densities as high as 5.3x10⁴ …

Benthic Foraminiferal Distributions In A Shallow Subtropical Estuary And The Influence Of Environmental Factors, Maria Angelica Zamora-Durán

Theses and Dissertations

Benthic foraminiferal communities are potentially useful tools for assessing and monitoring estuarine ecosystems and as bioindicators of water quality and pollution. To evaluate this indicator for the Indian River Lagoon (IRL) benthic ecosystem, the densities and distributions of Foraminifera were measured in Turkey Creek (Palm Bay, Florida), Crane Creek (Melbourne, Florida), and the adjacent IRL. Spatial population patterns were compared with parameters characterizing benthic sediments, including silt and clay content, organic matter (OM), and associated boundary water column conditions including salinity, temperature, and dissolved oxygen (DO. Samples (n=145) were collected from October 2015 to December 2015 at 12 locations. Four …

Digital Quorum Sensing For Self-Organizing Malware, Mark E. Fioravanti Ii

Theses and Dissertations

INTRODUCTION: Malware authors present an interesting problem for the security community as they evolve and adapt to overcome network and host defenses. The determined adversary is a special class of malware author who may attempt to disrupt national interests. These adversaries may seek potentially novel Command and Control (C2) channels to coordinate their activities. Isolated and air-gapped networks pose an interesting challenge that these adversaries must adapt to in order to maintain persistence on these networks. In this work we propose that a determined adversary may seek to implement a digital quorum sensing system inspired by the quorum sensing systems …

Robotic Arm Tracing Curves Recognized By Camera, Timothy Karl Findling

Theses and Dissertations

Applications such like soldering require robot arms to follow the soldering line as present on a surface. We assume here that the surface to be soldered is remote from the robotic arm, that the soldering is performed via a laser beam, and that the line to be followed can be a curve that may self-intersect (e.g. a crack in the material). We describe research conducted using a robotic arm pointing a laser for tracing a remote line on a smooth surface. The image of the line is converted to a one pixel width skeleton line generated from images using a …

Cross-Spectral Biometric Performance Analysis On High-Resolution Face Images, Praveen Kumar Pandian Shanmuganathan

Theses and Dissertations

Biometrics is increasingly being used to authenticate the identity of individuals in critical use case devices like smart phones, laptops, and several other access-control systems in our day-to-day lives. Additionally, biometrics is also used in forensic and security sensitive areas to detect and identify suspects involved in bombings, robberies, and several police investigations. In each of these critical scenarios, the high-quality full-frontal face images of the subjects are not accurately captured as those subjects do not intend to register their identity to the Closed-Circuit Cameras. Hence in such cases, identification of the suspects becomes difficult even though we have the …

Simulation Of Value Stream Mapping And Discrete Optimization Of Energy Consumption In Modular Construction, Md Mukul Chowdhury

Theses and Dissertations

With the increased practice of modularization and prefabrication, the construction industry gained the benefits of quality management, improved completion time, reduced site disruption and vehicular traffic, and improved overall safety and security. Whereas industrialized construction methods, such as modular and manufactured buildings, have evolved over decades, core techniques used in prefabrication plants vary only slightly from those employed in traditional site-built construction. With a focus on energy and cost efficient modular construction, this research presents the development of a simulation, measurement and optimization system for energy consumption in the manufacturing process of modular construction. The system is based on Lean …