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Engineering Of A Knowledge Management System For Relational Medical Diagnosis, Maria Carolina Herrera-Hernandez

USF Tampa Graduate Theses and Dissertations

The increasingly high costs of health care in the U.S. have led the general public to search for different medical approaches. Since the 1990's, the use of Complementary and Alternative Medicine (CAM) has radically increased in the U.S. due to its approach to treat physical, mental, and emotional causes of illness. In 2009, the National Health Statistics reported the impact of CAM in the U.S. health care economy, with population expenditures of $14.8 billion out-of-pocket on natural Medicine and $12.4 billion out-of-pocket on visits to CAM providers as a complement to Western Medicine care.

CAM interconnects human functions to reach …

Use Of Statistical Analysis, Data Mining, Decision Analysis And Cost Effectiveness Analysis To Analyze Medical Data : Application To Comparative Effectiveness Of Lumpectomy And Mastectomy For Breast Cancer., Beatrice Ugiliweneza

Electronic Theses and Dissertations

Statistical models have been the first choice for comparative effectiveness in clinical research. Though effective, these models are limited when the data to be analyzed do not fit the assumed distributions; which is mostly the case when the study is not a clinical trial. In this project, data mining, decision analysis and cost effectiveness analysis methods were used to supplement statistical models in comparing lumpectomy to mastectomy for surgical treatment of breast cancer. Mastectomy has been the gold standard for breast cancer treatment for since the 1800s. In the 20th century, an equivalence of mastectomy and lumpectomy was established in …

Data-Intensive Computing For Bioinformatics Using Virtualization Technologies And Hpc Infrastructures, Pengfei Xuan

All Theses

The bioinformatics applications often involve many computational components and massive data sets, which are very difficult to be deployed on a single computing machine. In this thesis, we designed a data-intensive computing platform for bioinformatics applications using virtualization technologies and high performance computing (HPC) infrastructures with the concept of multi-tier architecture, which can seamlessly integrate the web user interface (presentation tier), scientific workflow (logic tier) and computing infrastructure (data/computing tier). We demonstrated our platform on two bioinformatics projects. First, we redesigned and deployed the cotton marker database (CMD) (http://www.cottonmarker.org), a centralized web portal in the cotton research community, using the …

Database Methods For Copy Number Variant Analysis Of One Hundred Disease Associated Genes In Human Congenital Heart Disease, Maureen E. Tuffnell

Master's Theses (2009 -)

Human genetic variation occurs more commonly than was recognized after the completion of the Human Genome Sequencing Project in 2003. Submicroscopic human DNA analysis has revealed copy number variation (CNV) as the deletion or duplication of a genomic region potentially affecting gene dosage. Advanced genetic research now includes the study of CNVs in diseased subject groups compared to in house controls or online published datasets of control CNV data. Research labs choose from different bioinformatic algorithms to make the copy number calls. Solutions for further processing the copy number data into quantifiable form require collaboration with data analysts and include …

Development Of Computational Tools And Resources For Systems Biology Of Bacterial Pathogens, Ranjit Kumar

Theses and Dissertations

Bacterial pathogens are a major cause of diseases in human, agricultural plants and farm animals. Even after decades of research they remain a challenge to health care as they are known to rapidly evolve and develop resistance to the existing drugs. Systems biology is an emerging area of research where all of the components of the system, their interactions, and the dynamics can be studied in a comprehensive, quantitative, and integrative fashion to generate predictive models. When applied to bacterial pathogenesis, systems biology approaches will help identify potential novel molecular targets for drug discovery. A pre-requisite for conducting systems analysis …

Do Medical Technology And Healthcare Spending Affect Health Outcomes?, Chandni V. Vaid

Honors Theses

Healthcare expenditures have been on the rise for many countries, especially for the developed countries. As of 2009, Japan, Australia and Canada are spending around 8 to 10% of their total GDP on healthcare, while the United States is currently up to 16%. One of the major factors contributing to increased expenditures on healthcare is the emergence of medical technology. Using data from the Organization for Economic Co-operation and Development (OECD), I empirically investigate the effects of medical technologies and healthcare expenditure on health outcomes for a group of 17 countries. Medical technology is measured by the number of MRI …

The Interaction Of Cofilin With The Actin Filament, Diana Wong

All Theses and Dissertations (ETDs)

The regulation of filamentous actin: F-actin) production from the polymerization of globular actin: G-actin) within the cell is critical for many cell functions. Since actin is found in all cells, understanding how actin-binding-proteins: ABPs) bind and how their regulating mechanisms work is not only important to the basics of cytoskeletal pathways, but also to understanding associated diseases and creating possible therapeutics to combat them. Cofilin is an ABP that plays an important part in the regulation process and in recent times, has come to be known as a player in maintaining a cell's homeostasis. It's activity has been shown to …

Diversified Ensemble Classifiers For Highly Imbalanced Data Learning And Their Application In Bioinformatics, Zejin Ding

Computer Science Dissertations

In this dissertation, the problem of learning from highly imbalanced data is studied. Imbalance data learning is of great importance and challenge in many real applications. Dealing with a minority class normally needs new concepts, observations and solutions in order to fully understand the underlying complicated models. We try to systematically review and solve this special learning task in this dissertation.
We propose a new ensemble learning framework—Diversified Ensemble Classifiers for Imbal-anced Data Learning (DECIDL), based on the advantages of existing ensemble imbalanced learning strategies. Our framework combines three learning techniques: a) ensemble learning, b) artificial example generation, and c) …

Graph Kernels And Applications In Bioinformatics, Marco Alvarez Vega

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Nowadays, machine learning techniques are widely used for extracting knowledge from data in a large number of bioinformatics problems. It turns out that in many of such problems, data observations can be naturally represented by discrete structures such as graphs, networks, trees, or sequences. For example, a protein can be seen as a cloud of interconnected atoms lying on a 3-dimensional space. The focus of this dissertation is on the development and application of machine learning techniques to bioinformatics problems wherein the data can be represented by graphs. In particular, we focus our attention on proteins, which are essential elements …

Bistro-Primer - Tool To Design And Validate Specific Pcr Primer Pairs For Phylogenetic Analysis, Praful Aggarwal

Master's Theses (2009 -)

Polymerase Chain Reaction is a widely used biological technique which helps in amplifying small quantities of DNA. These amplified DNA copies are then used in several other experiments like DNA sequencing, phylogenetic analysis, etc. PCR primers are short subsequences of nucleotides (basic unit of DNA) that help identify larger regions of the DNA sequence. They help in successfully amplifying the target DNA sequence by identifying complementary regions on the DNA template. Therefore, to successfully perform PCR it is imperative to design good quality primers.

PCR can be used for identifying the phylogenetic classification of an organism. For example, in an …

Study Of The Rate And Spectrum Of Spontaneous Mutations, Way Sung

Doctoral Dissertations

Mutations are the initial force responsible for all aspects of genetic variation, and are a central part to evolution in all organisms. Yet despite its importance, the previously high cost that is associated with surveying mutations at a genome-wide scale has limited the understanding of the mutation process in eukaryotes. However, recent high-throughput sequencing technology has greatly reduced the cost of surveying mutations. By applying high-throughput sequencing to mutation accumulation experiments, we have begun to characterize the genome-wide mutation spectrum of eukaryotes.

Across all eukaryotes, we observe a biased rate of G/C-> A/T mutations that exceeds the number of A/T- …

Phylogenetic Analysis Of Blacknose Dace (Rhinichthys) In West Virginia Streams, Samantha Taylor

Theses, Dissertations and Capstones

Blacknose dace (Rhinichthys) are one of the most common cyprinid fishes in eastern North America. They also have been a topic of debate for over 30 years because morphology-based systematics has failed to clearly define their taxa. Taxonomists classify the complex into two species and one subspecies: the eastern form, R. atratulus atratulus; and the western form R. obtusus obtusus, and southern form R. obtusus meleagris. This research uses the mitochondrial cytochrome b gene and genomic RAG 2 gene in a phylogenetic analysis to help clarify species relations according to differences between each current species. Maps have been created to …

The Advancement Of Mass Spectrometry-Based Hydroxyl Radical Protein Footprinting: Application Of Novel Analysis Methods To Model Proteins And Apolipoprotein E, Brian Gau

All Theses and Dissertations (ETDs)

Fast photochemical oxidation of proteins: FPOP) has shown great promise in the elucidation of the regions of a protein's structure that are changed upon interaction with other macromolecules, ligands, or by folding. The advantage of this protein footprinting method is that it utilizes the reactivity of hydroxyl radicals to stably modify solvent accessible residues non-specifically in a microsecond. The extent of *OH labeling at sites assays their solvent accessibility. We have corroborated the predicted profoundly short timescale of labeling empirically, by FPOP-labeling three oxidation-sensitive proteins and examining their global FPOP product outcomes. The novel test developed to validate conformational invariance …

Systematic Identification Of Independent Functional Non-Coding Rna Genes In Oxytricha Trifallax, Seolkyoung Jung

All Theses and Dissertations (ETDs)

Functional noncoding RNAs participate in a variety of biological processes: for example, modulating translation, catalyzing biochemical reactions, sensing environments etc. Independent of conventional approaches such as transcriptomics and computational comparative analysis, we took advantage of the unusual genomic organization of the ciliated unicellular protozoan Oxytricha trifallax to screen for eukaryotic independent functional noncoding RNA genes. The Oxytricha macronuclear genome consists of thousands of gene-sized "nanochromosomes", each of which usually contains only a single gene. Using a draft Oxytricha trifallax genome assembly and a custom-written noncoding nanochromosome classifier, we identified a subset of nanochromosomes that lack any detectable protein coding gene, …

Computational Methods For Accelerated Discovery And Characterization Of Genes In Emerging Model Organisms, Alan Kwan

All Theses and Dissertations (ETDs)

Cilia are evolutionarily conserved, complex, microtubule-based structures that protrude from many eukaryotic cells. In humans, cilia can be found on almost all cell types. The effect of abnormal or absent cilia has been established as the common underlying cause of a recently emerging class of genetic diseases collectively referred to as ciliopathies. The function and structure of cilia are conserved across all organisms with cilia. One of the most influential model systems used to study ciliopathies has been the ciliated green alga Chlamydomonas reinhardtii, an organism for which there is a sequenced genome with relatively few experimentally validated whole-gene annotations …

Protein-Dna Recognition Models For The Homeodomain And C2h2 Zinc Finger Transcription Factor Families, Ryan Christensen

All Theses and Dissertations (ETDs)

Transcription factors: TFs) play a central role in the gene regulatory network of each cell. They can stimulate or inhibit transcription of their target genes by binding to short, degenerate DNA sequence motifs. The goal of this research is to build improved models of TF binding site recognition. This can facilitate the determination of regulatory networks and also allow for the prediction of binding site motifs based only on the TF protein sequence. Recent technological advances have rapidly expanded the amount of quantitative TF binding data available. PBMs: Protein Binding Microarrays) have recently been implemented in a format that allows …

Quantitative Analysis Demonstrates Most Transcription Factors Require Only Simple Models Of Specificity, Yue Zhao

All Theses and Dissertations (ETDs)

Organisms must control their gene expression to properly respond to developmental, stress or other environmental cues. A key part of this process is transcriptional regulation, which is largely accomplished by a complex network of transcription factor proteins: TFs) interact with their specific binding sites in the genome. Understanding how TFs select correct binding sites out of the vast number of potential binding sites in the genome is a key challenge in molecular biology. Recently, unprecedented amount of quantitative binding data have become available as results of developments in high-throughput experimental techniques. However, interpretation of high-throughput binding data has proved to …

Protein Surface Characterization Using An Invariant Descriptor, Zainab Abu Deeb

Graduate Theses, Dissertations, and Problem Reports

A novel descriptor to characterize protein surfaces, and hence classify functionally similar proteins into functional families is proposed. The descriptor exploits the protein tertiary structure surface, locally and globally, to identify intra-family proteins. By using only sparse data based on the C-alpha atoms on the protein surface, we characterize the surface using different invariant descriptors, namely, distance distributions, residue co-occurrences, and distance-residue co-occurrences between all atoms confined to a particular patch. Using the method, proteins with very low sequence similarity were successfully classified into their functional families with a high degree of accuracy.