Physical Sciences and Mathematics Commons^™

A Hybrid Parallel Approach To High-Performance Compression Of Big Genomic Files And In Compresso Data Processing, Sandino N. Vargas Pérez

Dissertations

Due to the rapid development of high-throughput low cost Next-Generation Sequencing, genomic file transmission and storage is now one of the many Big Data challenges in computer science. Highly specialized compression techniques have been devised to tackle this issue, but sequential data compression has become increasingly inefficient and existing parallel algorithms suffer from poor scalability. Even the best available solutions can take hours to compress gigabytes of data, making the use of these techniques for large-scale genomics prohibitively expensive in terms of time and space complexity.

This dissertation responds to the aforementioned problem by presenting a novel hybrid parallel approach …

Structures Of Derived Graphs, Khawlah Hamad Alhulwah

Dissertations

One of the most familiar derived graphs are line graphs. The line graph L(G) of a graph G is the graph whose vertices are the edges of G where two vertices of L(G) are adjacent if and only if the corresponding edges of G are adjacent. One of the best- known results on the structure of line graphs deals with forbidden subgraphs by Beineke. A characterization of graphs whose line graph is Hamiltonian is due to Harary and Nash-Williams. Iterated line graphs of almost all connected graphs were shown to be Hamiltonian by Chartrand. The girth of a graph G …

Statistical And Clinical Equivalence Of Measurements, Puntipa Wanitjirattikal

Dissertations

This study proposes a test for statistical equivalence of two measurements. Typically, a new measurement process Υ is compared to an existing or standard measurement process Χ. We are assuming that Χ and Υ are measurements on the same scale. The paired t-test may be used to check for significant difference between (Χ, Υ) pairs. However, the paired t-test is intended to detect shift-type relationships of the form Υ=Χ+δ1 and may have low power for scale-type relations of the form Υ=γΧ.

We propose a test that has reasonable power to …

An Lntegrated Approach (Remote Sensing, Hydrogeology, Geotechnical, And Geoinformatics) To Assess And Monitor Fossil Aquifers And Associated Land Deformation Over The Arabian Peninsula, Abdullah Ghurmullah Saeed Othman

Dissertations

Deformational features such as subsidence, sinkholes, fissures, settling and cracks in buildings and structures, and earthquakes are being reported from many of the world’s arid lands, in areas where fossil aquifers are being excessively exploited. Using the Lower Mega Aquifer System (LMAS) in Arabia as a test site, I applied an integrated approach (remote sensing, geodesy, GIS, geology, hydrogeology, and geotechnical) to identify nature, intensity, spatial distribution, and factors controlling the observed deformation in the central (Al-Qassim and Ha'il regions; area: 16×10⁴ km²) and the northern (Wadi As-Sirhan Basin; area: ~10.9×10⁴ km²) Arabia. A four -fold approach was adopted to …

Ldentifying And Characterizing Cognitive Factors Significant To Practicing And Learning Meteorology, Peggy M. Mcneal

Dissertations

To see the world as a meteorologist, one must understand and interpret atmospheric processes through representations depicted on two-dimensional weather charts and maps that encode large amounts of spatial and numerical data. This is a cognitively demanding and spatially challenging task, especially for students with burgeoning levels of meteorology knowledge, who lack the expertise of practiced meteorologists that read such charts and maps with ease. With little prior work informing meteorology and meteorology education through a cognitive science lens, this study surveys the literature and follows models of discipline-based education and cognitive science research to identify the discrete intelligence factors …

Diagnostics For Choosing Between Stratified Logrank And Stratified Wilcoxon, Jhoanne Marsh C. Gatpatan

Dissertations

Martinez and Naranjo (2010) proposed a pretest for choosing between Logrank or Wilcoxon test in a two - sample case. However, in the presence of covariates, comparing two populations without adjusting for covariates would yield misleading results. In this study, we propose several pretests that will help the analyst decide to use stratified Logrank or stratified Wilcoxon tests in comparing two survival curves after covariates have been taken into account. Power performance of each adaptive test was done through simulations under PH and non-PH cases.

High Performance Computing Techniques For Analyzing Risky Decision Making, Vinay B. Gavirangaswamy

Dissertations

The process or activity of making choices when subject to gain or loss can be understood as risky decision making (RDM). Risky Decisions consists of outcomes of decisions that may probabilistically result in unfavorable results. Every organism that lives faces this challenge and recent research suggests that there is a computational process involved in making these decisions. This has led to new approaches in the study of RDM. My dissertation is towards contributing to expand on the existing knowledge of RDM processes.

The core contribution of my work is an analysis and development of high performance computing techniques that improves …

Color-Connected Graphs And Information-Transfer Paths, Stephen Devereaux

Dissertations

The Department of Homeland Security in the United States was created in 2003 in response to weaknesses discovered in the transfer of classied information after the September 11, 2001 terrorist attacks. While information related to national security needs to be protected, there must be procedures in place that permit access between appropriate parties. This two-fold issue can be addressed by assigning information-transfer paths between agencies which may have other agencies as intermediaries while requiring a large enough number of passwords and rewalls that is prohibitive to intruders, yet small enough to manage. Situations such as this can be represented by …

A Deep Learníng-Based Data Minimization Algorithm For Big Genomics Data In Support Of Lot And Secure Smart Health Services, Mohammed Aledhari

Dissertations

In the age of Big Genomics Data, institutes such as the National Human Genome Research Institute (NHGRI),1000-Genomes project, and the international cancer sequencing consortium are faced with the challenge of sharing large volumes of data between internationallydispersed sample collectors, data analyzers, and researchers, a process that up until now has been plagued by unreliable transfers and slow connection speeds. These occur due to the inherent throughput bottlenecks of traditional transfer technologies. One suggested solution is using the cloud as an infrastructure to solve the store and analysis challenges. However, the transfer and share of the genomics datasets between biological laboratories …

Dielectronic Recombination Calculations For Silicon-Like Ions And The S2+ Orion Nebula Abundance Conundrum, Jagjit Kaur

Dissertations

Modern astronomical spectroscopy and imaging data are of an unprecedented quality, and span the full electromagnetic spectrum. To take full advantage of these data and successfully model the physical conditions in and elemental abundances of astrophysical plasmas, an accurate and complete description of relevant atomic processes occurring in a wide range of cosmic environments is required. The primary focus of this project is to investigate one of the atomic processes, dielectronic recombination (DR), for the entire silicon-like isoelectronic sequence. Dielectronic recombination is generally the most important contribution to the total recombination rate of atomic ions. This study will serve as …

Structures Of Metallacarboranes And Coordination Complexes: Coordination Sensors Based On Rhodamine B And Quinolines, Agozie Nnaemeka Oyeamalu

Dissertations

Rhodamine-based ligands that can complex different metals has been designed and synthesized. Using Rhodamine B as starting material, we synthesized and characterized quinoline precursors as well as successfully carried out the oxidation of methyl and aldehyde groups on the quinoline ring, and on the hydroxyl moiety of the quinoline spirolactone ring. These turn-on/off rhodamine fluorescence probes sense Cr³⁺ and Ni²⁺ with high selectivity and sensitivity. These probes can be applied to detect other metal ions that are present in chemical, biological and environmental settings. They were designed to fluoresce when bonded to ions such as cyanide in detecting …

Time-Dependent Photoionization Of Gaseous Nebulae, Ehab Elsayed Elhoussieny Ahmed

Dissertations

We study time-dependent photoionization of gaseous nebulae, i.e. the physical conditions and spectra of astronomical plasmas photoionized by a time-dependent source of ionizing radiation. Our study proceeds in two chief steps: First, we start with a simplified model of plasmas of pure H. Second, we develop a more realistic model of plasmas composed of a mixture of chemical elements. For the first step, we wrote a time-dependent photoionization code (TDP) that solves the coupled system of equations for ionization, energy balance, and radiation transfer in their full time-dependent forms For the second step, we developed a more realistic code (TDXSTAR) …

Development Of Traditional And Rank-Based Algorithms For Linear Models With Autoregressive Errors And Multivariate Logistic Regression With Spatial Random Effects, Shaofeng Zhang

Dissertations

Linear models are the most commonly used statistical methods in many disciplines. One of the model assumptions is that the error terms (residuals) are independent and identically distributed. This assumption is often violated and autoregressive error terms are often encountered by researchers. The most popular technique to deal with linear models with autoregressive errors is perhaps the autoregressive integrated moving average (ARIMA). Another common approach is generalized least squares, such as Cochrane-Orcutt estimation and Prais-Winsten estimation. However, these usually have poor behaviors when fitting small samples. To address this problem, a double bootstrap method was proposed by McKnight et al. …

Spatial Analysis Of Time Between Two Consecutive Dental And Two Consecutive Well-Child Visits For Foster Care Youth, Chenyang Shi

Dissertations

Foster care youth is a medically vulnerable population. Poor dental health and irregular well-child visits may cause serious health-related issues, such as mental disorder, nutrition imbalance, tooth damage, etc. Michigan requires all youth in foster care to receive annual dental and well-child visits. Usually, the study of foster care well-child and dental visits include two parts: time between two consecutive visits (gap time) and number of visits. For this study, a longitudinal-spatial model that has the flexibility to analyze the well-child/dental gap times and number of visits was developed. The longitudinal data (2009-2012) on Michigan foster care youth from 10 …

Chemotypic Variation Of Biogenic Volatile Organic Compounds In Midwest Forest And Atmospheric Role Of Peroxyacyl Nitrates In Southeastern U.S., Shino Toma

Dissertations

Biogenic volatile organic compounds (VOC), including isoprene and terpenes, impact atmospheric processes such as production of tropospheric ozone, formation and growth of secondary organic aerosol (SOA), global climate change, and human health. Although estimated emission rates of total biogenic VOC exceed anthropogenic emissions, there are many challenges to direct measurements because they are very reactive with atmospheric oxidants and some are still difficult to detect by current analytical techniques. Therefore, high uncertainties lead to discrepancies between individual and total biogenic VOC budget with atmospheric oxidants and an underestimation of SOA formation.

White pine (Pinus strobus) was once a dominant species …

Highly Hamiltonian Graphs And Digraphs, Zhenming Bi

Dissertations

A cycle that contains every vertex of a graph or digraph is a Hamiltonian cycle. A graph or digraph containing such a cycle is itself called Hamiltonian. This concept is named for the famous Irish physicist and mathematician Sir William Rowan Hamilton. These graphs and digraphs have been the subject of study for over six decades. In this dissertation, we study graphs and digraphs with even stronger Hamiltonian properties, namely highly Hamiltonian graphs and digraphs.

Artificial Immune Systems: Applications, Multi-Class Classification, Optimizations, And Analysis, Brian Haroldo Schmidt

Dissertations

The focus of this research is the application of the Artificial Immune System (AIS) paradigm to a new research area along with the modifications necessary to adapt it to a new problem. In the past 10 years, there has been much research into the use of various Machine Learning (ML) algorithms in Network Flow Traffic Classification. AIS algorithms have thus far not been applied to this problem. Because AIS algorithms have been used extensively for Network Intrusion Detection applications, which is a similar area of research, the motivation to extend them to the network flow classification problem is clear.

This …

Subgroup Analysis And Growth Curve Models For Longitudinal Data, Nichole Andrews

Dissertations

In clinical trials and biomedical studies, treatments are compared to determine which one is effective against illness. Growth curve analysis can be beneficial in longitudinal biomedical studies, as we can evaluate the treatment effect on the response over time. The generalized growth curve model using polynomial regression is proposed for longitudinal data. An optimal degree for the polynomial is obtained using the BIQIF, an adaptation of the Bayesian information criterion. Quadratic inference functions are used to estimate the parameters of the model, which takes into account the fact that repeated measurements from the same subject are more likely to be …

Protecting Sensitive Data In Clouds Using Active Data Bundles And Agent-Based Secure Multi-Party Computation, Akram Y. Sarhan

Dissertations

Protection of data in cloud computing including distributed environments is a critical concern for many enterprises. This study proposes a solution that protects sensitive data outsourced to a cloud throughout their entire life cycle—both in the cloud as well as outside of the cloud (e.g., during transmission to or from the cloud). The solution enhances the existing data protection approach known as Active Bundle scheme, which uses a Trusted Third Party (ABTTP).

The Active Data Bundle (ADB) was formerly called an Active Bundle (AB). It is a software construct that encapsulates data, metadata, and a virtual machine (VM). The metadata …

Biosorption Of Pharmaceuticals And Noble Metals Nanoparticles By Algal Turf Communities, Haider Abid Faraj

Dissertations

Pharmaceuticals and nanoparticles are increasingly released into the aquatic ecosystem, while removing these contaminants from waters can be challenging. This study explores the use of periphytic algal turf communities to remove these contaminants. Initially algal turfs from different locations and aquatic systems were analyzed for pharmaceuticals commonly observed in wastewater outflows. Lab-grown turfs were exposed to a mixture of six representative pharmaceuticals of different functionality (acid, base, neutral and steroidal). Analysis of water column and the algal biomass showed pharmaceutical removal rates varied, specific to each pharmaceutical. Caffeine and estradiol had the highest removal rates while carbamazepine was not removed. …