Data Science Commons^™

Statistical Methods For Resolving Intratumor Heterogeneity With Single-Cell Dna Sequencing, Alexander Davis

Dissertations and Theses (Open Access)

Tumor cells have heterogeneous genotypes, which drives progression and treatment resistance. Such genetic intratumor heterogeneity plays a role in the process of clonal evolution that underlies tumor progression and treatment resistance. Single-cell DNA sequencing is a promising experimental method for studying intratumor heterogeneity, but brings unique statistical challenges in interpreting the resulting data. Researchers lack methods to determine whether sufficiently many cells have been sampled from a tumor. In addition, there are no proven computational methods for determining the ploidy of a cell, a necessary step in the determination of copy number. In this work, software for calculating probabilities from …

Covid-19 Testnorm: A Tool To Normalize Covid-19 Testing Names To Loinc Codes, Xiao Dong, Jianfu Li, Ekin Soysal, Jiang Bian, Scott L Duvall, Elizabeth Hanchrow, Hongfang Liu, Kristine E Lynch, Michael Matheny, Karthik Natarajan, Lucila Ohno-Machado, Serguei Pakhomov, Ruth Madeleine Reeves, Amy M Sitapati, Swapna Abhyankar, Theresa Cullen, Jami Deckard, Xiaoqian Jiang, Robert Murphy, Hua Xu

Faculty, Staff and Student Publications

Large observational data networks that leverage routine clinical practice data in electronic health records (EHRs) are critical resources for research on coronavirus disease 2019 (COVID-19). Data normalization is a key challenge for the secondary use of EHRs for COVID-19 research across institutions. In this study, we addressed the challenge of automating the normalization of COVID-19 diagnostic tests, which are critical data elements, but for which controlled terminology terms were published after clinical implementation. We developed a simple but effective rule-based tool called COVID-19 TestNorm to automatically normalize local COVID-19 testing names to standard LOINC (Logical Observation Identifiers Names and Codes) …

Prediction Of Feed Utilization Performance In Clarias Gariepinus Using Multiple Linear Regression In Machine Learning, Adekunle Oluwatosin Familusi

Journal of Bioresource Management

Machine learning models can be used to make predictions about nutrient utilization performance index using available proximate analysis data on feed composition. Data from similar experiments on nutrient utilization performance was used to fit a multiple linear regression model for the prediction of four performance indexes. The Specific Growth Rate and percentage inclusion with strength of 0.57 was noted along with a negative relationship between protein efficiency and protein content. A negative relationship between Nitrogen Free Extract (NFE) and Protein Efficiency Ratio (PER) at NFE content ≥25 % was observed. PER was predicted with 85 % accuracy, while Weight Gain …

Surviving Under The Reign Of El Niño Southern Oscillation: An Analysis Of The Effects Of Extreme El Niño Events On The Oceanographic And Biological Environment Of The Galápagos Islands, Ava Mcilvaine

Independent Study Project (ISP) Collection

El Niño Southern Oscillation (ENSO) is commonly known as the atmospheric and oceanographic powerhouse of the Southern Pacific Ocean. From phytoplankton to apex predators, ENSO controls the stability of species’ populations within this biodiverse ocean environment. El Niño’s 9-15 month alteration of the heat storage in the tropical Pacific drastically shifts the temperature, nutrient, and circulation gradient its marine life is accustomed to. A single degree change in the ocean’s surface layer temperature can have large consequences for marine species, and El Niño is commonly associated with Sea Surface Temperature Anomalies (SSTAs) between 2°- 6° Celsius. The potential danger El …

An Apex Predator In Peril In The Western Lowlands Of Ecuador: Mapping The Population Distribution Of Harpy Eagles (Harpia Harpyja) In A Highly Deforested Region, Samuel Zhang

Independent Study Project (ISP) Collection

The Harpy Eagle (Harpia harpyja) is a highly threatened bird of prey in Ecuador. While they are already elusive in the Ecuadorian Amazon, they are even lesser known in the coastal lowlands, and their existence is threatened by rapid deforestation. This study mapped their potential distribution by examining satellite images to find intact humid forest, their ideal habitat. Habitat areas were quantified using ImageJ. The only sites found to be adequate for sustaining Harpy Eagle populations were the primary forests in the vicinities of Reserva Ecológica Mache Chindul and Reserva Ecológica Cotacachi Cayapas. The two reserves are expected to be …

Two (Or More) Viruses In One Bat: A Systematic Quantitative Literature Review Of Viral Coinfection In Bats, Eli J. Kaufman

Independent Study Project (ISP) Collection

Viral coinfection is an important topic in pathogen dynamics, and can increase viral shedding and change disease outcomes. As bats are carriers of important zoonoses, such as the SARS coronaviruses, rabies, and other deadly viruses, knowing more about their coinfection dynamics is important. This quantitative systematic literature review sought to show how many papers reported bat viral coinfections, and created three databases. The first database, the SQLR database was based on searches for coinfections. The second database, the Astrovirus database was to determine how much of the literature was being missed by examining a single viral family more in depth …

Deep Learning In Clinical Natural Language Processing: A Methodical Review, Stephen Wu, Kirk Roberts, Surabhi Datta, Jingcheng Du, Zongcheng Ji, Yuqi Si, Sarvesh Soni, Qiong Wang, Qiang Wei, Yang Xiang, Bo Zhao, Hua Xu

Faculty, Staff and Student Publications

OBJECTIVE: This article methodically reviews the literature on deep learning (DL) for natural language processing (NLP) in the clinical domain, providing quantitative analysis to answer 3 research questions concerning methods, scope, and context of current research.

MATERIALS AND METHODS: We searched MEDLINE, EMBASE, Scopus, the Association for Computing Machinery Digital Library, and the Association for Computational Linguistics Anthology for articles using DL-based approaches to NLP problems in electronic health records. After screening 1,737 articles, we collected data on 25 variables across 212 papers.

RESULTS: DL in clinical NLP publications more than doubled each year, through 2018. Recurrent neural networks (60.8%) …

A Novel Item-Allocation Procedure For The Three-Form Planned Missing Data Design, Kyle M. Lang, E. Whitney G. Moore, Elizabeth M. Grandfield

Kinesiology, Health and Sport Studies

We propose a new method of constructing questionnaire forms in the three-form planned missing data design (PMDD). The random item allocation (RIA) procedure that we propose promises to dramatically simplify the process of implementing three-form PMDDs without compromising statistical performance. Our method is a stochastic approximation to the currently recommended approach of deterministically spreading a scale's items across the X-, A-, B-, and C-blocks when allocating the items in a three-form design. Direct empirical support for the performance of our method is only available for scales containing at least 12 items, so we also propose a modified approach for use …

An Analytical Examination On The Effects Of Vegetarian And Omnivorous Diets On C-Reactive Protein, Aletha Kleis

Undergraduate Honors Theses

There is a lack of research regarding how following a vegetarian or omnivores diet effects C-Reactive Protein (CRP) levels of people as seen through results from an analysis of data gathered from the National Health and Nutrition Examination Survey (NHANES). The level of CRP is a reflection of how much inflammation there is in one’s body and is a popular indicator of risk for heart disease. Thus, in this research, I use the NHANES data to look at the relationship of CRP levels of people who identified themselves as vegetarian or not, while also considering the general healthiness of each …

Prospects And Challenges Of Population Health With Online And Other Big Data In Africa; Understanding The Link To Improving Healthcare Service Delivery, Rowland Edet, Bolarinwa Afolabi

Department of Sociology: Faculty Publications

Big data analytics offers promises to many health care service challenges and can provide answers to many population health issues. Big data is having a positive impact in almost every sphere of life in more advanced world while developing countries are striving to meet up. Even though healthcare systems in the developed world are recording some breakthroughs due to the application of big data, it is important to research the impact of big data in developing regions of the world, such as Africa and identify its peculiar needs. The purpose of this review was to summarize the challenges faced by …

Digilego For Peripartum Depression: A Novel Patient-Facing Digital Health Instantiation, J Rodin, C Timko, S Harris

Faculty, Staff and Student Publications

Digital health technologies offer unique opportunities to improve health outcomes for mental health conditions such as peripartum depression (PPD), a disorder that affects approximately 10-15% of women in the U.S. every year. In this paper, we present the adaption of a digital technology development framework, Digilego, in the context of PPD. Methods include mapping of the Behavior Intervention Technology (BIT) model and the Patient Engagement Framework (PEF) to translate patient needs captured through focus groups. This informs formative development and implementation of digital health features for optimal patient engagement in PPD screening and management. Results show an array ofPPD-specific Digilego …

Deconvolution Tools For Extracting Insight From Challenging Two-Flavin Systems, Dallas Michael Bell

Theses and Dissertations--Chemistry

Flavoproteins have long been explored for their ubiquity among a number of metabolic and energetic reactions. The flavin cofactor has the inherent benefit of distinct spectral changes associated with redox transitions; however, the double-edged sword is incurred as these distinct signatures overlap and take up much of the UV-vis spectral range. Therefore, it is crucial to create a method to demarcate the expressed redox transitions for studying these systems. The first portion of these studies discusses the creation of a program that deduces spectra for redox transitions in a single-flavin containing model protein: flavodoxin. The latter portions discuss the application …

Causal Discovery In Radiographic Markers Of Knee Osteoarthritis And Prediction For Knee Osteoarthritis Severity With Attention-Long Short-Term Memory, Yanfei Wang, Lei You, Jacqueline Chyr, Lan Lan, Weiling Zhao, Yujia Zhou, Hua Xu, Philip Noble, Xiaobo Zhou

Faculty, Staff and Student Publications

The goal of this study is to build a prognostic model to predict the severity of radiographic knee osteoarthritis (KOA) and to identify long-term disease progression risk factors for early intervention and treatment. We designed a long short-term memory (LSTM) model with an attention mechanism to predict Kellgren/Lawrence (KL) grade for knee osteoarthritis patients. The attention scores reveal a time-associated impact of different variables on KL grades. We also employed a fast causal inference (FCI) algorithm to estimate the causal relation of key variables, which will aid in clinical interpretability. Based on the clinical information of current visits, we accurately …

Enhancing Clinical Concept Extraction With Contextual Embeddings, Yuqi Si, Jingqi Wang, Hua Xu, Kirk Roberts

Faculty, Staff and Student Publications

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 …

What About The Environment?: Exploring The Neglected Third Dimension Of Antimicrobial Resistance, Paige E. Montfort

Independent Study Project (ISP) Collection

Antimicrobial resistance (AMR) is one of the most urgent and complex health risks of our time, with links to human health, animal health, and the environment. The majority of research and policy related to AMR, however, has been dedicated to human and animal health. The third dimension — the environment — has been relatively neglected. Conversations about this problem have begun, but gaps in understanding remain. This study explores the key barriers that have hindered developments related to the environmental aspect of AMR and some of the solutions that have begun to or could be utilized to overcome these barriers. …

Precision Agriculture Gis Technologies For Mississippi, 1st. Edition, Amelia A.A. Fox

CALS Publications

Precision agriculture is meant to improve on-farm efficiency in hopes of ultimately increasing profitability while also protecting the environment. However, this difficult process almost always includes the proper management and interpretation of data. Therefore, it is imperative that those individuals involved in making such decisions are educated on these processes. In a data-driven world, this textbook is a great resource for those wanting to learn how to utilize their data in hopes of making better informed on-farm decisions.

Deep Patient Representation Of Clinical Notes Via Multi-Task Learning For Mortality Prediction, Yuqi Si, Kirk Roberts

Faculty, Staff and Student Publications

We propose a deep learning-based multi-task learning (MTL) architecture focusing on patient mortality predictions from clinical notes. The MTL framework enables the model to learn a patient representation that generalizes to a variety of clinical prediction tasks. Moreover, we demonstrate how MTL enables small but consistent gains on a single classification task (e.g., in-hospital mortality prediction) simply by incorporating related tasks (e.g., 30-day and 1-year mortality prediction) into the MTL framework. To accomplish this, we utilize a multi-level Convolutional Neural Network (CNN) associated with a MTL loss component. The model is evaluated with 3, 5, and 20 tasks and is …

Effects Of A Community Population Health Initiative On Blood Pressure Control In Latinos, James R Langabeer, Timothy D Henry, Carlos Perez Aldana, Larissa Deluna, Nora Silva, Tiffany Champagne-Langabeer

Faculty, Staff and Student Publications

Background Hypertension remains one of the most important, modifiable cardiovascular risk factors. Yet, the largest minority ethnic group (Hispanics/Latinos) often have different health outcomes and behavior, making hypertension management more difficult. We explored the effects of an American Heart Association-sponsored population health intervention aimed at modifying behavior of Latinos living in Texas. Methods and Results We enrolled 8071 patients, and 5714 (65.7%) completed the 90-day program (58.5 years ±11.7; 59% female) from July 2016 to June 2018. Navigators identified patients with risk factors; initial and final blood pressure ( BP ) readings were performed in the physician's office; and interim …

Estimating Exploitation Rates In The Alabama Red Snapper Fishery Using A High-Reward Tag–Recapture Approach, Dana K. Sackett, Mattgew Catalano, J. Marcus Drymon, Sean P. Powers, Mark Albins

University Faculty and Staff Publications

Accurate estimates of exploitation are essential to managing an exploited fishery. However, these estimates are often dependent on the area and vulnerable sizes of fish considered in a study. High-reward tagging studies offer a simple and direct approach to estimating exploitation rates at these various scales and in examining how model parameters impact exploitation rate estimates. These methods can ultimately provide a better understanding of the spatial dynamics of exploitation at smaller local and regional scales within a fishery—a measure often needed for more site-attached species, such as the Red Snapper Lutjanus campechanus. We used this approach to tag 724 …

Compression And Relaxation Of Fishing Effort In Response To Changes In Length Of Fishing Season For Red Snapper (Lutjanus Campechanus) In The Northern Gulf Of Mexico, Sean P. Powers, Kevin Anson

University Faculty and Staff Publications

A standard method used by fisheries managers to decrease catch and effort is to shorten the length of a fishery; however, data on recreational angler response to this simple approach are surprisingly lacking. We assessed the effect of variable season length on daily fishing effort, measured by using numbers of boat launches per day, anglers per boat, and anglers per day from video observations, in the recreational sector of the federal fishery for red snapper (Lutjanus campechanus) in coastal Alabama. From 2012 through 2017, season length fluctuated from 3 to 40 d. Daily effort, measured by using mean number of …

A Frame-Based Nlp System For Cancer-Related Information Extraction, Yuqi Si, Kirk Roberts

Faculty, Staff and Student Publications

We propose a frame-based natural language processing (NLP) method that extracts cancer-related information from clinical narratives. We focus on three frames: cancer diagnosis, cancer therapeutic procedure, and tumor description. We utilize a deep learning-based approach, bidirectional Long Short-term Memory (LSTM) Conditional Random Field (CRF), which uses both character and word embeddings. The system consists of two constituent sequence classifiers: a frame identification (lexical unit) classifier and a frame element classifier. The classifier achieves an F

The Utility Of Bioenergetics Modelling In Quantifying Predation Rates Of Marine Apex Predators: Ecological And Fisheries Implications, A. Barnett, M. Braccini, C. L. Dudgeon, N. L. Payne, K. G. Abrantes, M. Sheaves, E. P. Snelling

Fisheries Research Articles

Predators play a crucial role in the structure and function of ecosystems. However, the magnitude of this role is often unclear, particularly for large marine predators, as predation rates are difficult to measure directly. If relevant biotic and abiotic parameters can be obtained, then bioenergetics modelling offers an alternative approach to estimating predation rates, and can provide new insights into ecological processes. We integrate demographic and ecological data for a marine apex predator, the broadnose sevengill shark Notorynchus cepedianus, with energetics data from the literature, to construct a bioenergetics model to quantify predation rates on key fisheries species in …

Survey Results: Complexities And Overlaps In Existing Citizen Science Mosquito Projects, Yujia He, Elizabeth Tyson

Patterson School of Diplomacy and International Commerce Faculty Publications

Currently, multiple projects worldwide engage the public in the scientific process of learning about mosquito biodiversity or monitoring mosquitoes that carry diseases like Dengue, Chikungunya, Zika and Malaria. These projects are executed at different invasion-stages and different scenarios of epidemiological risk based on their country of origin. Through surveying 12 international research teams, this brief report illuminates the differences and the overlaps in the protocols and tools used by existing citizen science mosquito monitoring projects. The analysis covers project goals, requirements and support for participants, policy impact, digital tools and data privacy.

Marine Ecoregion And Deepwater Horizon Oil Spill Affect Recruitment And Population Structure Of A Salt Marsh Snail, Steven C. Pennings, Scott Zengel, Jacob Oehrig, Merryl Alber, T. Dale Bishop, Donald R. Deis, Donna Devlin, A. Randall Hughes, John J. Hutchens, Jr., Whitney M. Kiehn, Caroline R. Mcfarlin, Clay L. Montague, Sean P. Powers, C. Edward Proffitt, Nicholle Rutherford, Camille L. Stagg, Keith Walters

University Faculty and Staff Publications

Marine species with planktonic larvae often have high spatial and temporal variation in recruitment that leads to subsequent variation in the ecology of benthic adults. Using a combination of published and unpublished data, we compared the population structure of the salt marsh snail, Littoraria irrorata, between the South Atlantic Bight and the Gulf Coast of the United States to infer geographic differences in recruitment and to test the hypothesis that the Deepwater Horizon oil spill led to widespread recruitment failure of L. irrorata in Louisiana in 2010. Size-frequency distributions in both ecoregions were bimodal, with troughs in the distributions consistent …

The Role Of Citizens In Detecting And Responding To A Rapid Marine Invasion, Steven B. Scyphers, Sean P. Powers, J. Lad Akins, J. Marcus Drymon, Charles W. Martin, Zeb H. Schobernd, Pamela J. Schofield, Robert L. Shipp, Theodore S. Switzer

University Faculty and Staff Publications

Documenting and responding to species invasions requires innovative strategies that account for ecological and societal complexities. We used the recent expansion of Indo-Pacific lionfish (Pterois volitans/miles) throughout northern Gulf of Mexico coastal waters to evaluate the role of stakeholders in documenting and responding to a rapid marine invasion. We coupled an online survey of spearfishers and citizen science monitoring programs with traditional fishery-independent data sources and found that citizen observations documented lionfish 1–2 years earlier and more frequently than traditional reef fish monitoring programs. Citizen observations first documented lionfish in 2010 followed by rapid expansion and proliferation in …

Reasoning Over Taxonomic Change: Exploring Alignments For The Perelleschus Use Case, Nico M. Franz, Mingmin Chen, Shizhuo Yu, Parisa Kianmajd, Shaun Bowers, Bertram Ludäscher

Computer Science Faculty Scholarship

Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted …

Scalable Combinatorial Tools For Health Disparities Research, Michael A. Langston, Robert S. Levine, Barbara J. Kilbourne, Gary L. Rogers Jr., Anne D. Kershenbaum, Suzanne H. Baktash, Steven S. Coughlin, Arnold M. Saxton, Vincent K. Agboto, Darryl B. Hood, Maureen Y. Litchveld, Tonny J. Oyana, Patricia Matthews-Juarez, Paul D. Juarez

Sociology Faculty Research

Despite staggering investments made in unraveling the human genome, current estimates suggest that as much as 90% of the variance in cancer and chronic diseases can be attributed to factors outside an individual’s genetic endowment, particularly to environmental exposures experienced across his or her life course. New analytical approaches are clearly required as investigators turn to complicated systems theory and ecological, place-based and life-history perspectives in order to understand more clearly the relationships between social determinants, environmental exposures and health disparities. While traditional data analysis techniques remain foundational to health disparities research, they are easily overwhelmed by the ever-increasing size …

Data Completion Methods For Improved Developmental Stage Annotation Of Drosophila Embryos In Images, Chitsanu Janyalikit

Electrical & Computer Engineering Theses & Dissertations

Drosophila melanogaster is a dominant model organism for studying the function of animal genes in initial stages of embryogenesis. Usually, images containing Drosophila gene expression patterns are captured at different developmental stages to study the interconnection of animal genes. To achieve most biologically meaningful results, gene expression images from a similar stage should be compared. Currently, biologists manually classify embryos in images into different stages, which is time intensive and infeasible for current massively produced gene expression images. Therefore, there is a need to develop an automatic system for the annotation.

Gene expression information in embryo images usually appears as …

Integrating Societal Perspectives And Values For Improved Stewardship Of A Coastal Ecosystem Engineer, Steven B. Scyphers, J. Steven Picou, Robert D. Brumbaugh, Sean P. Powers

University Faculty and Staff Publications

Oyster reefs provide coastal societies with a vast array of ecosystem services, but are also destructively harvested as an economically and culturally important fishery resource, exemplifying a complex social-ecological system (SES). Historically, societal demand for oysters has led to destructive and unsustainable levels of harvest, which coupled with multiple other stressors has placed oyster reefs among the most globally imperiled coastal habitats. However, more recent studies have demonstrated that large-scale restoration is possible and that healthy oyster populations can be sustained with effective governance and stewardship. However, both of these require significant societal support or financial investment. In our study, …

Semantics In Support Of Biodiversity Knowledge Discovery: An Introduction To The Biological Collections Ontology And Related Ontologies, Ramona L. Walls, John Deck, Robert Guralnick, Steve Baskauf, Reed Beaman, Stanley Blum, Shaun Bowers

Computer Science Faculty Scholarship

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to …