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Articles 1 - 30 of 199
Full-Text Articles in Life Sciences
Cancer Risk Prediction With Whole Exome Sequencing And Machine Learning, Abdulrhman Fahad M Aljouie
Cancer Risk Prediction With Whole Exome Sequencing And Machine Learning, Abdulrhman Fahad M Aljouie
Dissertations
Accurate cancer risk and survival time prediction are important problems in personalized medicine, where disease diagnosis and prognosis are tuned to individuals based on their genetic material. Cancer risk prediction provides an informed decision about making regular screening that helps to detect disease at the early stage and therefore increases the probability of successful treatments. Cancer risk prediction is a challenging problem. Lifestyle, environment, family history, and genetic predisposition are some factors that influence the disease onset. Cancer risk prediction based on predisposing genetic variants has been studied extensively. Most studies have examined the predictive ability of variants in known …
Connectivity Differences Between Gulf War Illness (Gwi) Phenotypes During A Test Of Attention, Tomas Clarke, Jessie Jamieson, Patrick Malone, Rakib U. Rayhan, Stuart Washington, John W. Vanmeter, James N. Baraniuk
Connectivity Differences Between Gulf War Illness (Gwi) Phenotypes During A Test Of Attention, Tomas Clarke, Jessie Jamieson, Patrick Malone, Rakib U. Rayhan, Stuart Washington, John W. Vanmeter, James N. Baraniuk
Department of Mathematics: Faculty Publications
One quarter of veterans returning from the 1990–1991 Persian Gulf War have developed Gulf War Illness (GWI) with chronic pain, fatigue, cognitive and gastrointestinal dysfunction. Exertion leads to characteristic, delayed onset exacerbations that are not relieved by sleep. We have modeled exertional exhaustion by comparing magnetic resonance images from before and after submaximal exercise. One third of the 27 GWI participants had brain stem atrophy and developed postural tachycardia after exercise (START: Stress Test Activated Reversible Tachycardia). The remainder activated basal ganglia and anterior insulae during a cognitive task (STOPP: Stress Test Originated Phantom Perception). Here, the role of attention …
A Transcriptomic Exploration Of Hawaiian Drosophilid Development And Evolution, Madeline M. Chenevert
A Transcriptomic Exploration Of Hawaiian Drosophilid Development And Evolution, Madeline M. Chenevert
University of New Orleans Theses and Dissertations
One in four known species of fruit flies inhabit the Hawaiian Islands. From a small number of colonizing flies, a wide range of species evolved, some of which managed to reverse-colonize other continental environments. In order to explore the developmental pathways, which separate the Hawaiian Drosophila proper and the Scaptomyza group that contains reverse-colonized species, the transcriptomes of two better-known species in each group, Scaptomyza anomala and Drosophila grimshawi, were analyzed to find changes in gene expression between the two groups. This study describes a novel transcriptome for S. anomala studies as well as unusual changes in gene expression …
A Landscape On The Threshold Of Change: Patterns Of Soil Microbial Ecology Along Dynamic Geomorphic And Hydrologic Features In A Polar Desert, Kelli L. Feeser, David J. Van Horn, Heather N. Buelow, Daniel R. Colman, Theresa A. Mchugh, Jordan G. Okie, Egbert Schwartz, Cristina D. Takacs-Vesbach, Becky A. Ball, Andrew G. Fountain, Michael N. Gooseff, Joseph S. Levy, Maciej K. Obryk
A Landscape On The Threshold Of Change: Patterns Of Soil Microbial Ecology Along Dynamic Geomorphic And Hydrologic Features In A Polar Desert, Kelli L. Feeser, David J. Van Horn, Heather N. Buelow, Daniel R. Colman, Theresa A. Mchugh, Jordan G. Okie, Egbert Schwartz, Cristina D. Takacs-Vesbach, Becky A. Ball, Andrew G. Fountain, Michael N. Gooseff, Joseph S. Levy, Maciej K. Obryk
Biology ETDs
The McMurdo Dry Valleys (MDV) of Antarctica are on the threshold of widespread landscape scale change due to increasing temperature and solar radiation and altered hydrology: buried ice is melting, the soil active layer is thickening, thermokarst features are developing along streams, water tracks are expanding, and lake levels are rising. These changes will impact the microbial communities found in each of the affected habitats. The purpose of this work is to first, understand the spatial distribution of soil bacteria in the MDV, specifically investigating the scale-dependent effects of environmental heterogeneity, and second, to perform surveys and coupled experiments to …
Early Child Development Amid The Pandemic, Zain Saeed Siddiqui
Early Child Development Amid The Pandemic, Zain Saeed Siddiqui
MSJ Capstone Projects
I would like to bring to notice the importance of early child development because the early years are crucial for the development especially the skills that are going to help children succeed in life. Basically, I would like to focus on the natural development of the human being from birth to maturity, enabling children to become the transforming elements of society, leading to a harmonious and peaceful world.
Emotional well-being and social competence provide a strong foundation for emerging cognitive abilities, and together they are the bricks and mortar that comprise the foundation of human development.
Generally, development happens in …
Phylogenetic And Genomic Characterization Of The Host-Pathogen Arms Race Between Bacterial Pathogens And Gossypium Hirsutum, Anne Zimmerman Phillips
Phylogenetic And Genomic Characterization Of The Host-Pathogen Arms Race Between Bacterial Pathogens And Gossypium Hirsutum, Anne Zimmerman Phillips
Arts & Sciences Electronic Theses and Dissertations
Hosts and pathogens are eternally intertwined in an evolutionary arms race. When a pathogen causes a disease outbreak, scientists must identify resistance strategies that can durably tilt the arms race in favor of the host. This requires a deep understanding of both the genetic and environmental contexts in which the outbreak occurs. In this thesis I investigate the bacterial pathogens Xanthomonas citri pv. malvacearum (Xcm) and Pseudomonas syringae that caused disease outbreaks on Gossypium hirsutum from 2011-2017. I use pathogen genomics and host transcriptomics to develop hypotheses for how these pathogens emerged and how they cause disease. Phylogenetics and virulence …
Physiologic And Pathologic Profiling Of Clonal Variations, Wing Hing Wong
Physiologic And Pathologic Profiling Of Clonal Variations, Wing Hing Wong
Arts & Sciences Electronic Theses and Dissertations
This thesis sought to provide a better understanding of clonality in various malignant and non-malignant settings using a variety of genomic analytical tools. Clonality is pre-defined as the presence of a mixed population of cells in which each sub-population has distinct somatic mutation profile. It is a common feature in cancers where subpopulations of cells arise as a result of independent, yet continual acquisition of somatic mutations. The clonal architecture of cancers can be used as a diagnostic and prognostic biomarker as well as to monitor disease progression or resolution. Besides cancer, clonal variability and expansion is also implicated in …
Vaxinsight: An Artificial Intelligence System To Access Large-Scale Public Perceptions Of Vaccination From Social Media, Jingcheng Du
Vaxinsight: An Artificial Intelligence System To Access Large-Scale Public Perceptions Of Vaccination From Social Media, Jingcheng Du
Dissertations & Theses (Open Access)
Vaccination is considered one of the greatest public health achievements of the 20th century. A high vaccination rate is required to reduce the prevalence and incidence of vaccine-preventable diseases. However, in the last two decades, there has been a significant and increasing number of people who refuse or delay getting vaccinated and who prohibit their children from receiving vaccinations. Importantly, under-vaccination is associated with infectious disease outbreaks. A good understanding of public perceptions regarding vaccinations is important if we are to develop effective vaccination promotion strategies. Traditional methods of research, such as surveys, suffer limitations that impede our understanding of …
Mechanisms And Consequences Of Myb Gene Activation In Salivary Gland Tumors, Candace Frerich
Mechanisms And Consequences Of Myb Gene Activation In Salivary Gland Tumors, Candace Frerich
Biomedical Sciences ETDs
Salivary gland adenoid cystic carcinoma (ACC) is an aggressive tumor with a tendency to infiltrate surrounding nerves and metastasize to distant sites. The standard treatment often fails to control local tumor recurrence and distant metastases and no approved targeted therapeutic options exist for these tumors. The goal of our studies was to reveal the molecular mechanisms driving ACC tumor development and novel drug targets to improve patient morbidity and mortality.
We first analyzed clinical and RNA-sequencing (RNA-seq) data for 68 formalin-fixed paraffin-embedded (FFPE) ACC tumor samples and described previously unappreciated molecular heterogeneity that predicts patient outcome. The poor outcome subgroup …
Finding And Analyzing De Novo Mutations In The Exomes Of Parent-Offspring Trios Of Spontaneous Chiari Malformation Type 1 Patients, Brian Leon Ricardo
Finding And Analyzing De Novo Mutations In The Exomes Of Parent-Offspring Trios Of Spontaneous Chiari Malformation Type 1 Patients, Brian Leon Ricardo
Arts & Sciences Electronic Theses and Dissertations
Chiari Malformation Type 1 (CM1) is a neurodevelopmental disorder that occurs when one of the cerebellar tonsils herniates past the foramen magnum causing headaches, motor or sensory deficits, sleep apnea, and difficulty swallowing. This disorder is estimated to affect 1% of the population but due to the need of neuroimaging for diagnosis and the presence of asymptomatic patients there is still uncertainty about the exact proportion of the population affected. CM1 often presents itself with other neurodevelopmental disorders such as syringomyelia, scoliosis, and known genetic syndromes such as Klippel-Feil and Marfan syndromes. Twin, family, and familial clustering studies have established …
The Effect Of Historic Shipwrecks On Sediment Microbiomes In The Northern Gulf Of Mexico, Melissa Brock
The Effect Of Historic Shipwrecks On Sediment Microbiomes In The Northern Gulf Of Mexico, Melissa Brock
Master's Theses
Microorganisms are ubiquitously distributed across all aquatic habitats, but it is the environmental conditions of a habitat that determine which microorganisms can thrive in terms of abundance or metabolic activity. Habitats that experience consistent physical and chemical environmental conditions repeatedly favor specific taxonomic groups which may result in a microbial assemblage that is commonly associated with that habitat (i.e., a core microbiome). Core microbiomes have been identified for a variety of natural marine habitats including methane seeps, wood falls, octocoral, and deep-sea sediments. However, it was unknown if the presence of man-made structures on the seafloor, including historic shipwrecks, also …
The Antimicrobial Activity And Cellular Targets Of Plant Derived Aldehydes And Degradable Pro-Antimicrobial Networks In Pseudomonas Aeruginosa, Yetunde Adewunmi
The Antimicrobial Activity And Cellular Targets Of Plant Derived Aldehydes And Degradable Pro-Antimicrobial Networks In Pseudomonas Aeruginosa, Yetunde Adewunmi
Dissertations
Essential oils (EOs) are plant-derived products that have been long exploited for their antimicrobial activities in medicine, agriculture, and food preservation. EOs represent a promising alternative to conventional antibiotics due to the broad-range antimicrobial activity, low toxicity to human commensal bacteria, and the capacity to kill microorganisms without promoting resistance. Despite the progress in the understanding of the biological activity of EOs, many aspects of their mode of action remain inconclusive. The overarching aim of this work was to address these gaps by studying molecular interactions between antimicrobial plant aldehydes and the opportunistic human pathogen Pseudomonas aeruginosa. We initiated …
The Identification Of Long Non-Coding Rna Zfas1 Through An Exploratory Rna-Sequencing Analysis And Its Association With Epithelial-To-Mesenchymal Transition In Colon Cancer Adenocarcinoma., Stephen J. O'Brien
Electronic Theses and Dissertations
Colorectal adenocarcinoma is the fourth most common cancer diagnosed worldwide and is a significant cause of morbidity and mortality. This dissertation performed an exploratory RNA-sequencing analysis comparing gene expression between colon adenocarcinoma tissue and paired normal colon epithelium. After identification of a number of lncRNAs that were increased in expression in colon adenocarcinoma compared to normal colon epithelium, we aimed to validate the expression and investigate their function in vitro. Specifically, we focused on the lncRNA ZFAS1 and its association with epithelial-to-mesenchymal transition. These studies found the following: 1. Seven candidate lncRNAs were identified from the exploratory RNA-sequencing analysis to …
Discovery Of An Egfr Inhibitor For The Treatment Of Lung And Other Cancers, Jodie Meng '20
Discovery Of An Egfr Inhibitor For The Treatment Of Lung And Other Cancers, Jodie Meng '20
Student Publications & Research
The Epidermal Growth Factor Receptor (EGFR), a transmembrane protein involved in the regulation of signaling pathways, is frequently overexpressed in epithelial tumors. First generation EGFR TKIs, such as erlotinib and gefitinib, traditionally improved outcomes for non-small-cell lung carcinoma and pancreatic cancer patients by attaching competitively and reversibly to the ATP binding domain of EGFR. Second-generation EGFR TKIs have been developed to combat resistance among patients, despite demonstrating toxic side effects. In the present study, 1400 selective inhibitors were designed based on the molecular scaffolds of first and second generation EGFR TKIs. Results were refined by parameters outlined in Lipinski’s rule. …
Enhancing Clinical Concept Extraction With Contextual Embeddings., Yuqi Si, Jingqi Wang, Hua Xu, Kirk Roberts
Enhancing Clinical Concept Extraction With Contextual Embeddings., Yuqi Si, Jingqi Wang, Hua Xu, Kirk Roberts
Journal Articles
OBJECTIVE: Neural network-based representations ("embeddings") have dramatically advanced natural language processing (NLP) tasks, including clinical NLP tasks such as concept extraction. Recently, however, more advanced embedding methods and representations (eg, ELMo, BERT) have further pushed the state of the art in NLP, yet there are no common best practices for how to integrate these representations into clinical tasks. The purpose of this study, then, is to explore the space of possible options in utilizing these new models for clinical concept extraction, including comparing these to traditional word embedding methods (word2vec, GloVe, fastText).
MATERIALS AND METHODS: Both off-the-shelf, open-domain embeddings and …
Transcriptomic Analyses And Computational Modeling Reveal That Fatty Acid Transport Protein 2 (Fatp2) Impacts The Transcriptional Activity Of Pparα Thus Altering The Lipid Metabolic Landscape, Vincent M. Perez
Department of Biochemistry: Dissertations, Theses, and Student Research
Fatty acid transport protein 2 (FATP2) is highly expressed in liver, small intestine, and kidney where it functions in both the uptake of exogenous long chain fatty acids (LCFAs) and in the activation of very long chain fatty acids (VLCFAs). Here we address the phenotypic impacts of deleting FATP2 with the following three separate approaches: [1] Utilizing an unbiased next-generation sequencing analysis of FATP2-null (fatp2-/-) mice fed a standard chow diet; [2] Utilizing an unbiased next-generation sequencing analysis of fatp2-null (fatp2-/-) mice fed a high-fat ketogenic diet (KD) and fasted for 24-hours [3] Building dynamic computer models built with data …
Game-Assisted Rehabilitation For Post-Stroke Survivors, Hee-Tae Jung
Game-Assisted Rehabilitation For Post-Stroke Survivors, Hee-Tae Jung
Doctoral Dissertations
Stroke is a leading cause of permanent impairments among its survivors. Although patients need to go through intensive, longitudinal rehabilitation to regain function before the stroke, patients show poor engagement and adherence to rehabilitation therapies which hampers their recovery. As a means to enhance stroke survivors' motivation, engagement, and adherence to intensive and longitudinal rehabilitation, the use of games in stroke rehabilitation has received attention from research and clinical communities. In order to realize this, it is important to take a holistic, end-to-end research approach that encompasses 1) the development of game technologies that are not only entertaining but also …
Tal Effector-Nucleotide Targeter (Tale-Nt) 2.0: Tools For Tal Effector Design And Target Prediction, Erin L. Doyle, Nicholas J. Booher, Daniel S. Standage, Daniel F. Voytas, Volker P. Brendel, John K. Vandyk, Adam J. Bogdanove
Tal Effector-Nucleotide Targeter (Tale-Nt) 2.0: Tools For Tal Effector Design And Target Prediction, Erin L. Doyle, Nicholas J. Booher, Daniel S. Standage, Daniel F. Voytas, Volker P. Brendel, John K. Vandyk, Adam J. Bogdanove
Nicholas J. Booher
Transcription activator-like (TAL) effectors are repeat-containing proteins used by plant pathogenic bacteria to manipulate host gene expression. Repeats are polymorphic and individually specify single nucleotides in the DNA target, with some degeneracy. A TAL effector-nucleotide binding code that links repeat type to specified nucleotide enables prediction of genomic binding sites for TAL effectors and customization of TAL effectors for use in DNA targeting, in particular as custom transcription factors for engineered gene regulation and as site-specific nucleases for genome editing. We have developed a suite of web-based tools called TAL Effector-Nucleotide Targeter 2.0 (TALE-NT 2.0;https://boglab.plp.iastate.edu/) that enables design …
Enhancing Timeliness Of Drug Overdose Mortality Surveillance: A Machine Learning Approach, Patrick J. Ward, Peter J. Rock, Svetla Slavova, April M. Young, Terry L. Bunn, Ramakanth Kavuluru
Enhancing Timeliness Of Drug Overdose Mortality Surveillance: A Machine Learning Approach, Patrick J. Ward, Peter J. Rock, Svetla Slavova, April M. Young, Terry L. Bunn, Ramakanth Kavuluru
Kentucky Injury Prevention and Research Center Faculty Publications
BACKGROUND: Timely data is key to effective public health responses to epidemics. Drug overdose deaths are identified in surveillance systems through ICD-10 codes present on death certificates. ICD-10 coding takes time, but free-text information is available on death certificates prior to ICD-10 coding. The objective of this study was to develop a machine learning method to classify free-text death certificates as drug overdoses to provide faster drug overdose mortality surveillance.
METHODS: Using 2017–2018 Kentucky death certificate data, free-text fields were tokenized and features were created from these tokens using natural language processing (NLP). Word, bigram, and trigram features were created …
Scl: A Lattice-Based Approach To Infer 3d Chromosome Structures From Single-Cell Hi-C Data, Hao Zhu, Zheng Wang
Scl: A Lattice-Based Approach To Infer 3d Chromosome Structures From Single-Cell Hi-C Data, Hao Zhu, Zheng Wang
Student Publications
Motivation: In contrast to population-based Hi-C data, single-cell Hi-C data are zero-inflated and do not indicate the frequency of proximate DNA segments. There are a limited number of computational tools that can model the 3D structures of chromosomes based on single-cell Hi-C data.
Results: We developed single-cell lattice (SCL), a computational method to reconstruct 3D structures of chromosomes based on single-cell Hi-C data. We designed a loss function and a 2 D Gaussian function specifically for the characteristics of single-cell Hi-C data. A chromosome is represented as beads-on-a-string and stored in a 3 D cubic lattice. Metropolis–Hastings simulation …
Molecular Phylogeny Implemented In An Introductory Plant Classification Course, Chao Cai, Jo Ann Banks
Molecular Phylogeny Implemented In An Introductory Plant Classification Course, Chao Cai, Jo Ann Banks
Libraries Faculty and Staff Presentations
Plant classification is one of the core components in undergraduate programs related to plant sciences. Traditionally plant classification courses primarily introduce morphology-based taxonomy because of practical needs in the field. However, the publication of new plant classification systems by Angiosperm Phylogeny Group (APG) using molecular phylogeny methods leads to the trends of using molecular evidence (DNA barcode) for plant identification. In our introductory plant classification course, we included a two-week module (lectures and labs) to introduce key concepts and fundamental skills in molecular phylogeny. Week 1 included concepts of evolutionary tree thinking, data mining in NCBI using BLAST search, and …
Sdrap: An Annotation Pipeline For Highly Scrambled Genomes, Jasper Braun
Sdrap: An Annotation Pipeline For Highly Scrambled Genomes, Jasper Braun
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
Network Reconstruction Using Computational Algebra And Gene Knockouts, Matthew Macauley
Network Reconstruction Using Computational Algebra And Gene Knockouts, Matthew Macauley
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
Loop Homology Of Bi-Secondary Structures, Andrei Bura
Loop Homology Of Bi-Secondary Structures, Andrei Bura
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
The Energy-Spectrum Of Bicompatible Sequences, Wenda Huang
The Energy-Spectrum Of Bicompatible Sequences, Wenda Huang
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
On An Enhancement Of Rna Probing Data Using Information Theory, Thomas J.X. Li, Christian M. Reidys
On An Enhancement Of Rna Probing Data Using Information Theory, Thomas J.X. Li, Christian M. Reidys
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
Evidence For Adaptive Introgression Of Exons Across A Hybrid Swarm In Deer, Emily Latch, Margaret Haines, Gordon Luikart, Stephen Amish, Seth Smith
Evidence For Adaptive Introgression Of Exons Across A Hybrid Swarm In Deer, Emily Latch, Margaret Haines, Gordon Luikart, Stephen Amish, Seth Smith
Biological Sciences Faculty Articles
Background: Secondary contact between closely related lineages can result in a variety of outcomes, including hybridization, depending upon the strength of reproductive barriers. By examining the extent to which different parts of the genome introgress, it is possible to infer the strength of selection and gain insight into the evolutionary trajectory of lineages. Following secondary contact approximately 8000 years ago in the Pacific Northwest, mule deer (Odocoileus hemionus hemionus) and black-tailed deer (O. h. columbianus) formed a hybrid swarm along the Cascade mountain range despite substantial differences in body size (up to two times) and habitat preference. In this study, …
36 Years After The Species' Mass-Mortality: Diadema Antillarum Test Sizes, Population Densities, And Substrate Preferences In Three Guna Yala Reefs Near Wichub Wala Island, Bimini Horstmann
Independent Study Project (ISP) Collection
In January 1983, a waterborne pathogen beginning near the Atlantic Panama Canal entrance caused history's largest recorded marine animal die-off, wiping out 95-99% of Diadema antillarum populations throughout the Caribbean. D. antillarum, the long-spined sea urchin, is a keystone herbivore in coral reefs and its decreased densities have caused many reefs to suffer macroalgal phase shifts. Modest recovery of this species has been documented in some Caribbean locations, but reefs in Guna Yala, Panama continued to experience population decline. This study investigates density, test size, and substrate preferences of D. antillarum in three shallow coral reef areas to update the …
From Traps To Snapshots: Examining The Ecology Of Feral Predators And Native Small Mammals In Southeastern Australia Through Case Studies Of Two Faunal Sampling Methods, Katherine Karson
Independent Study Project (ISP) Collection
The red fox (Vulpes vulpes) and feral cat (Felis catus) are introduced mesopredators that significantly threaten native small mammal species in Australia. For decades, environmental managers have attempted to mitigate the effects of these introduced species. However, ecosystems are highly complex, making it difficult to assess the impacts of feral predators on communities of native fauna independent of other disturbances such as fire regime and habitat fragmentation. Cost-effective ecological monitoring programs are imperative for evaluating threats to native species and informing environmental decisions. New technology has become increasingly present in wildlife monitoring, and camera trapping has provided an alternative to …
Optimizing Water Quality And Temperature Parameters To Increase Survival Rates Of Anotheca Spinosa (Anura: Hylidae) Eggs At The El Valle Amphibian Conservation Center, Morgan Oestereich
Optimizing Water Quality And Temperature Parameters To Increase Survival Rates Of Anotheca Spinosa (Anura: Hylidae) Eggs At The El Valle Amphibian Conservation Center, Morgan Oestereich
Independent Study Project (ISP) Collection
Amphibians globally are facing extinction due to the fungus Batrachochytrium dendrobatidis (Bd). This has resulted in a worldwide push for increased conservation efforts. These efforts include those of the El Valle Amphibian Conservation Center (EVACC) in El Valle de Antón, Panama, where captive assurance colonies of many native amphibian species are housed. Among these species is Anotheca spinosa, a species of tree frog native to mountainous regions of Central America. This study was performed to analyze the relationship between water quality parameters and egg survival and reproductive success of EVACC’s captive population of A. spinosa and assess how related husbandry …