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Phr: Patient Health Record, Quinn Nelson 2018 University of Nebraska at Omaha

Phr: Patient Health Record, Quinn Nelson

Theses/Capstones/Creative Projects

The rapid development of information technology systems has expanded into multiple disciplines and results in systems that are limited by initial design and implementation: the Healthcare Information Technology (HIT) space is no different. The introduction of the Electronic Health Record (EHR) system has changed the way healthcare operates. Initial designs of these systems were focused on serving the needs of insurance companies and healthcare billing departments. Research shows that the design of EHR systems negatively impact provider-patient interactions and the care they receive. This capstone project capitalizes on the collaboration efforts between UNO and UNMC – by joining a research group ...


Color Space Standardization And Image Analysis For High-Throughput Phenotyping Of Sorghum Bicolor, Alexandria A. Pokorny 2018 Department of Mathematics, Illinois State University

Color Space Standardization And Image Analysis For High-Throughput Phenotyping Of Sorghum Bicolor, Alexandria A. Pokorny

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Using Canalization For The Control Of Discrete Networks, David Murrugarra 2018 University of Kentucky

Using Canalization For The Control Of Discrete Networks, David Murrugarra

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Using Non Stem-Cells To Understand Early Tumor Growth, Jake Hogan, Heiko Enderling, Joel Brown, Robert A. Gatenby 2018 Brigham Young University

Using Non Stem-Cells To Understand Early Tumor Growth, Jake Hogan, Heiko Enderling, Joel Brown, Robert A. Gatenby

Library/Life Sciences Undergraduate Poster Competition 2018

Tumors of similar size and shape can exhibit different responses to the same treatment. Targeted therapy aims to better treat these tumors by classifying them according to genotypic traits. A better understanding of how tumor traits such as non-stem cells influence tumor growth could improve targeted therapy. We hypothesize that the production of non-stem cells may aid tumor growth in avascular tumors (tumors lacking blood vessels).


Identification And Characterization Of Nitrogen Fixing Bacteria Associated With Kudzu Root Nodules, Chasity Lawless, Michelle Zedonek, Debbie Curtis, Jonda Scharringhausen, Jared Bryant, Wendy A. Dustman, Alexandra M. Kurtz, Bekah Ward Dr. 2018 Georgia Gwinnett College

Identification And Characterization Of Nitrogen Fixing Bacteria Associated With Kudzu Root Nodules, Chasity Lawless, Michelle Zedonek, Debbie Curtis, Jonda Scharringhausen, Jared Bryant, Wendy A. Dustman, Alexandra M. Kurtz, Bekah Ward Dr.

Georgia Journal of Science

Pueraria montana, better known as kudzu, is an invasive species rapidly spreading throughout the southeastern United States. This plant can form root nodules which house nitrogen-fixing bacteria, allowing atmospheric nitrogen to be converted into biologically available forms of nitrogen for use by the plant host. Given the centrality of these bacteria to the spread of kudzu, isolates from nodules were characterized after collection from seven different locations across the metropolitan Atlanta area. Twenty-five isolates were grown on two different variants of nitrogen free media. Four different carbon sources were evaluated as well. Finally, growth under both aerobic and anaerobic conditions ...


Confirming World-Wide Distribution Of An Agriculturally Important Lacewing, Chrysoperla Zastrowi Sillemi, Using Songs, Morphology, Mitochondrial Gene Sequencing, And Phylogenetic Reconstruction, Zoe Mandese 2018 University of Connecticut

Confirming World-Wide Distribution Of An Agriculturally Important Lacewing, Chrysoperla Zastrowi Sillemi, Using Songs, Morphology, Mitochondrial Gene Sequencing, And Phylogenetic Reconstruction, Zoe Mandese

Honors Scholar Theses

The Chrysoperla carnea-group of green lacewings is a cryptic species complex. Species within the group are morphologically similar, yet isolated from one another via reproductive mating song. Chrysoperla zastrowi, a species within the carnea-group, is currently described with a distribution ranging from South Africa to the Middle East and India. However, recent collections of carnea-group lacewings from Guatemala and California were preliminarily identified as Chrysoperla zastrowi based upon similarities in their vibrational courtship songs. This analysis aims to place six specimens, collected by collaborators in Guatemala, Armenia, Iran, and California, into a pre-existing phylogeny of the Chrysoperla ...


Computational Analysis Of Genomic Variants Affecting Predicted Microrna:Target Interactions In Prostate Cancer., Angélica Paola Hernández Pérez 2018 Keck Graduate Institute, KGI

Computational Analysis Of Genomic Variants Affecting Predicted Microrna:Target Interactions In Prostate Cancer., Angélica Paola Hernández Pérez

KGI Theses and Dissertations

Prostate cancer (PCa) is the most common cancer of men in the United States and is third only to lung and colon as a cause of cancer death. Clinical behavior of the disease is variable and the combination of prostate-specific antigen (PSA) screening and Gleason score staging are currently the best available molecular and pathology tools to predict outcomes. Cancer biology research establishes microRNAs (miRNAs) as key molecular components in both normal and pathological states. Thus, elucidating miRNAs perturbed by genomic alterations will expand our understanding of the molecular taxonomy of PCa with the aim to complement current practices in ...


The Temporal Landscape Of Recursive Splicing During Pol Ii Transcription Elongation In Human Cells, Xiao-Ou Zhang, Yu Fu, Haiwei Mou, Wen Xue, Zhiping Weng 2018 University of Massachusetts Medical School

The Temporal Landscape Of Recursive Splicing During Pol Ii Transcription Elongation In Human Cells, Xiao-Ou Zhang, Yu Fu, Haiwei Mou, Wen Xue, Zhiping Weng

Program in Bioinformatics and Integrative Biology Publications and Presentations

Recursive splicing (RS) is an evolutionarily conserved process of removing long introns via multiple steps of splicing. It was first discovered in Drosophila and recently proven to occur also in humans. The detailed mechanism of recursive splicing is not well understood, in particular, whether it is kinetically coupled with transcription. To investigate the dynamic process that underlies recursive splicing, we systematically characterized 342 RS sites in three human cell types using published time-series data that monitored synchronized Pol II elongation and nascent RNA production with 4-thiouridine labeling. We found that half of the RS events occurred post-transcriptionally with long delays ...


Differential Analysis Of Chromatin Accessibility And Histone Modifications For Predicting Mouse Developmental Enhancers, Shaliu Fu, Qin Wang, Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Kaili Fan, Cuihua Gu, Cizhong Jiang, Ruixin Zhu, Anshul Kundaje, Aiping Lu, Zhiping Weng 2018 Tongji University,China

Differential Analysis Of Chromatin Accessibility And Histone Modifications For Predicting Mouse Developmental Enhancers, Shaliu Fu, Qin Wang, Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Kaili Fan, Cuihua Gu, Cizhong Jiang, Ruixin Zhu, Anshul Kundaje, Aiping Lu, Zhiping Weng

Program in Bioinformatics and Integrative Biology Publications and Presentations

Enhancers are distal cis-regulatory elements that modulate gene expression. They are depleted of nucleosomes and enriched in specific histone modifications; thus, calling DNase-seq and histone mark ChIP-seq peaks can predict enhancers. We evaluated nine peak-calling algorithms for predicting enhancers validated by transgenic mouse assays. DNase and H3K27ac peaks were consistently more predictive than H3K4me1/2/3 and H3K9ac peaks. DFilter and Hotspot2 were the best DNase peak callers, while HOMER, MUSIC, MACS2, DFilter and F-seq were the best H3K27ac peak callers. We observed that the differential DNase or H3K27ac signals between two distant tissues increased the area under the precision-recall ...


A Mechanism Of Antimicrobial Resistance And A Mitigation Strategy, Christopher Bulow 2018 Washington University in St. Louis

A Mechanism Of Antimicrobial Resistance And A Mitigation Strategy, Christopher Bulow

Arts & Sciences Electronic Theses and Dissertations

ABSTRACT OF THE DISSERTATION

A Mechanism of Antimicrobial Resistance and a Mitigation Strategy

by

Christopher Bulow

Doctor of Philosophy in Biology and Biomedical Sciences

Molecular Genetics and Genomics

Washington University in St. Louis, 2018

Professor Gautam Dantas, Chair

The ability to treat infections, perform surgery, and administer immunosuppressants and chemotherapy depends on effective antibiotics. The emergence and spread of antimicrobial resistance is far outpacing the development of new therapies1-3 threatening to thrust medicine into a post-antibiotic era4. Many mechanisms of antimicrobial action and of antimicrobial resistance remain poorly understood as drug development struggles to keep pace. As resistance develops, the ...


Drug-Resistance And Population Structure Of Plasmodium Falciparum Across The Democratic Republic Of Congo Using High-Throughput Molecular Inversion Probes, Ozkan Aydemir, Nicholas J. Hathaway, Patrick W. Marsh, Alice Tran, Thomas Reimonn, Jeffrey A. Bailey 2018 University of Massachusetts Medical School

Drug-Resistance And Population Structure Of Plasmodium Falciparum Across The Democratic Republic Of Congo Using High-Throughput Molecular Inversion Probes, Ozkan Aydemir, Nicholas J. Hathaway, Patrick W. Marsh, Alice Tran, Thomas Reimonn, Jeffrey A. Bailey

Open Access Articles

A better understanding of the drivers of the spread of malaria parasites and drug resistance across space and time is needed. These drivers can be elucidated using genetic tools. Here, a novel molecular inversion probe (MIP) panel targeting all major drug-resistance mutations and a set of microsatellites was used to genotype Plasmodium falciparum infections of 552 children from the 2013-2014 Demographic and Health Survey conducted in the Democratic Republic of the Congo (DRC). Microsatellite-based analysis of population structure suggests that parasites within the DRC form a homogeneous population. In contrast, sulfadoxine-resistance markers in dihydropteroate synthase show marked spatial structure with ...


Microbial Ecology Of South Florida Surface Waters: Examining The Potential For Anthropogenic Influences, Chase P. Donnelly 2018 Nova Southeastern University

Microbial Ecology Of South Florida Surface Waters: Examining The Potential For Anthropogenic Influences, Chase P. Donnelly

HCNSO Student Theses and Dissertations

South Florida contains one of the largest subtropical wetlands in the world, and yet not much is known about the microbes that live in these surface waters. These microbes play an important role in chemical cycling and maintaining good water quality for both human and ecosystem health. The hydrology of Florida’s surface waters is tightly regulated with the use of canal and levee systems run by the US Army Corps of Engineers and The South Florida Water Management District. These canals run through the Everglades, agriculture, and urban environments to control water levels in Lake Okeechobee, the Water Conservation ...


Genome Analysis Of Multiple Mycobacteriophage, Emily Kerstiens, Kari Clase, Yi Li, Gillian Smith, Sarah Bell 2018 Purdue University

Genome Analysis Of Multiple Mycobacteriophage, Emily Kerstiens, Kari Clase, Yi Li, Gillian Smith, Sarah Bell

The Summer Undergraduate Research Fellowship (SURF) Symposium

Bacteriophage are viruses that infect and kill bacteria. They can be used as treatments for antibiotic resistant bacterial infections, but more knowledge is needed about phage and how they interact with bacteria in order to develop safe and effective phage therapy treatments. This study examines the genomes of eighteen mycobacteriophage that were isolated from the environment on and surrounding Purdue University. Phage genomes were annotated using several bioinformatics software, including DNA Master, GeneMark, and PECAAN. Evidence was examined to determine the correct location within the genome and the potential function. Approximately two thousand genes were annotated in this study. A ...


Bayesian Analytical Approaches For Metabolomics : A Novel Method For Molecular Structure-Informed Metabolite Interaction Modeling, A Novel Diagnostic Model For Differentiating Myocardial Infarction Type, And Approaches For Compound Identification Given Mass Spectrometry Data., Patrick J. Trainor 2018 University of Louisville

Bayesian Analytical Approaches For Metabolomics : A Novel Method For Molecular Structure-Informed Metabolite Interaction Modeling, A Novel Diagnostic Model For Differentiating Myocardial Infarction Type, And Approaches For Compound Identification Given Mass Spectrometry Data., Patrick J. Trainor

Electronic Theses and Dissertations

Metabolomics, the study of small molecules in biological systems, has enjoyed great success in enabling researchers to examine disease-associated metabolic dysregulation and has been utilized for the discovery biomarkers of disease and phenotypic states. In spite of recent technological advances in the analytical platforms utilized in metabolomics and the proliferation of tools for the analysis of metabolomics data, significant challenges in metabolomics data analyses remain. In this dissertation, we present three of these challenges and Bayesian methodological solutions for each. In the first part we develop a new methodology to serve a basis for making higher order inferences in metabolomics ...


Deciphering The Role Of Human Arylamine N-Acetyltransferase 1 (Nat1) In Breast Cancer Cell Metabolism Using A Systems Biology Approach., Samantha Marie Carlisle 2018 University of Louisville

Deciphering The Role Of Human Arylamine N-Acetyltransferase 1 (Nat1) In Breast Cancer Cell Metabolism Using A Systems Biology Approach., Samantha Marie Carlisle

Electronic Theses and Dissertations

Background: Human arylamine N-acetyltransferase 1 (NAT1) is a phase II xenobiotic metabolizing enzyme found in almost all tissues. NAT1 can additionally hydrolyze acetyl-coenzyme A (acetyl-CoA) in the absence of an arylamine substrate. NAT1 expression varies inter-individually and is elevated in several cancers including estrogen receptor positive (ER+) breast cancers. Additionally, multiple studies have shown the knockdown of NAT1, by both small molecule inhibition and siRNA methods, in breast cancer cells leads to decreased invasive ability and proliferation and decreased anchorage-independent colony formation. However, the exact mechanism by which NAT1 expression affects cancer risk and progression remains unclear. Additionally, consequences ...


Extending Chemical Perturbations Of The Ubiquitin Fitness Landscape In A Classroom Setting Reveals New Constraints On Sequence Tolerance, David Mavor, Daniel N. Bolon, Martin Kampmann, James S. Fraser 2018 University of California, San Francisco

Extending Chemical Perturbations Of The Ubiquitin Fitness Landscape In A Classroom Setting Reveals New Constraints On Sequence Tolerance, David Mavor, Daniel N. Bolon, Martin Kampmann, James S. Fraser

Open Access Articles

Although the primary protein sequence of ubiquitin (Ub) is extremely stable over evolutionary time, it is highly tolerant to mutation during selection experiments performed in the laboratory. We have proposed that this discrepancy results from the difference between fitness under laboratory culture conditions and the selective pressures in changing environments over evolutionary timescales. Building on our previous work (Mavor et al., 2016), we used deep mutational scanning to determine how twelve new chemicals (3-Amino-1,2,4-triazole, 5-fluorocytosine, Amphotericin B, CaCl2, Cerulenin, Cobalt Acetate, Menadione, Nickel Chloride, p-Fluorophenylalanine, Rapamycin, Tamoxifen, and Tunicamycin) reveal novel mutational sensitivities of ubiquitin residues. Collectively, our ...


Collaborative Heroism: An Empirical Investigation, Dana Klisanin 2018 University of Richmond

Collaborative Heroism: An Empirical Investigation, Dana Klisanin

Heroism Science: An Interdisciplinary Journal

Interactive technologies have come to define our culture, and as such, they influence and shape our modes of perception and behavior. This empirical investigation explored the public’s perception of the impact of the Internet on heroism via assessment of a sample population through a process of item generation, sampling, and principal component analysis. A robust 5-component structure emerged with consensus among participants including: 1) Collaboration expands heroic potential; 2) Internet technology expands heroic potential; 3) Heroes are motivated to protect and serve; 4) Heroes are responsive to injustice; 5) Concern for others is a required ingredient. The results extend ...


Elimination Of Pcr Duplicates In Rna-Seq And Small Rna-Seq Using Unique Molecular Identifiers, Yu Fu, Pei-Hsuan Wu, Timothy J. Beane, Phillip D. Zamore, Zhiping Weng 2018 University of Massachusetts Medical School

Elimination Of Pcr Duplicates In Rna-Seq And Small Rna-Seq Using Unique Molecular Identifiers, Yu Fu, Pei-Hsuan Wu, Timothy J. Beane, Phillip D. Zamore, Zhiping Weng

Open Access Articles

BACKGROUND: RNA-seq and small RNA-seq are powerful, quantitative tools to study gene regulation and function. Common high-throughput sequencing methods rely on polymerase chain reaction (PCR) to expand the starting material, but not every molecule amplifies equally, causing some to be overrepresented. Unique molecular identifiers (UMIs) can be used to distinguish undesirable PCR duplicates derived from a single molecule and identical but biologically meaningful reads from different molecules.

RESULTS: We have incorporated UMIs into RNA-seq and small RNA-seq protocols and developed tools to analyze the resulting data. Our UMIs contain stretches of random nucleotides whose lengths sufficiently capture diverse molecule species ...


Elimination Of Pcr Duplicates In Rna-Seq And Small Rna-Seq Using Unique Molecular Identifiers, Yu Fu, Pei-Hsuan Wu, Timothy J. Beane, Phillip D. Zamore, Zhiping Weng 2018 University of Massachusetts Medical School

Elimination Of Pcr Duplicates In Rna-Seq And Small Rna-Seq Using Unique Molecular Identifiers, Yu Fu, Pei-Hsuan Wu, Timothy J. Beane, Phillip D. Zamore, Zhiping Weng

Program in Bioinformatics and Integrative Biology Publications and Presentations

BACKGROUND: RNA-seq and small RNA-seq are powerful, quantitative tools to study gene regulation and function. Common high-throughput sequencing methods rely on polymerase chain reaction (PCR) to expand the starting material, but not every molecule amplifies equally, causing some to be overrepresented. Unique molecular identifiers (UMIs) can be used to distinguish undesirable PCR duplicates derived from a single molecule and identical but biologically meaningful reads from different molecules.

RESULTS: We have incorporated UMIs into RNA-seq and small RNA-seq protocols and developed tools to analyze the resulting data. Our UMIs contain stretches of random nucleotides whose lengths sufficiently capture diverse molecule species ...


Dynamic Placement Of The Linker Histone H1 Associated With Nucleosome Arrangement And Gene Transcription In Early Drosophila Embryonic Development, Jian Hu, Liang Gu, Youqiong Ye, Meizhu Zheng, Zhu Xu, Jing Lin, Yanhua Du, Mengxue Tian, Lifang Luo, Beibei Wang, Xiaobai Zhang, Zhiping Weng, Cizhong Jiang 2018 Tongji University

Dynamic Placement Of The Linker Histone H1 Associated With Nucleosome Arrangement And Gene Transcription In Early Drosophila Embryonic Development, Jian Hu, Liang Gu, Youqiong Ye, Meizhu Zheng, Zhu Xu, Jing Lin, Yanhua Du, Mengxue Tian, Lifang Luo, Beibei Wang, Xiaobai Zhang, Zhiping Weng, Cizhong Jiang

Open Access Articles

The linker histone H1 is critical to maintenance of higher-order chromatin structures and to gene expression regulation. However, H1 dynamics and its functions in embryonic development remain unresolved. Here, we profiled gene expression, nucleosome positions, and H1 locations in early Drosophila embryos. The results show that H1 binding is positively correlated with the stability of beads-on-a-string nucleosome organization likely through stabilizing nucleosome positioning and maintaining nucleosome spacing. Strikingly, nucleosomes with H1 placement deviating to the left or the right relative to the dyad shift to the left or the right, respectively, during early Drosophila embryonic development. H1 occupancy on genic ...


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