Digital Commons Network^™

Leveraging Gpt-4 For Identifying Cancer Phenotypes In Electronic Health Records: A Performance Comparison Between Gpt-4, Gpt-3.5-Turbo, Flan-T5, Llama-3-8b, And Spacy's Rule-Based And Machine Learning-Based Methods, Kriti Bhattarai, Inez Y Oh, Jonathan Moran Sierra, Jonathan Tang, Philip R O Payne, Zach Abrams, Albert M Lai

2020-Current year OA Pubs

OBJECTIVE: Accurately identifying clinical phenotypes from Electronic Health Records (EHRs) provides additional insights into patients' health, especially when such information is unavailable in structured data. This study evaluates the application of OpenAI's Generative Pre-trained Transformer (GPT)-4 model to identify clinical phenotypes from EHR text in non-small cell lung cancer (NSCLC) patients. The goal was to identify disease stages, treatments and progression utilizing GPT-4, and compare its performance against GPT-3.5-turbo, Flan-T5-xl, Flan-T5-xxl, Llama-3-8B, and 2 rule-based and machine learning-based methods, namely, scispaCy and medspaCy.

MATERIALS AND METHODS: Phenotypes such as initial cancer stage, initial treatment, evidence of cancer recurrence, and affected …

Reproducibility And Repeatability Of Intervoxel Incoherent Motion Mri Acquisition Methods In Liver, Juan A. Vasquez, Marissa Brown, Mary Woolsey, Mohammad Abdul-Ghani, Venkata Katabathina, Shengwen Deng, John Blangero, Geoffrey D. Clarke

School of Medicine Publications

Background: Intravoxel incoherent motion (IVIM) diffusion weighted MRI (DWI) has potential for evaluating hepatic fibrosis but image acquisition technique influence on diffusion parameter estimation bears investigation.

Purpose: To minimize variability and maximize repeatably in abdominal DWI in terms of IVIM parameter estimates.

Study type: Prospective test-retest and image quality comparison.

Subjects: Healthy volunteers (3F/7M, 29.9 ± 12.9 years) and Family Study subjects (18F/12M, 51.7 ± 16.7 years), without and with liver steatosis.

Field strength/sequence: Abdominal single-shot echo-planar imaging (EPI) and simultaneous multi-slice (SMS) DWI sequences with respiratory triggering (RT), breath-holding (BH), and navigator echo (NE) at 3 Tesla.

Assessment: SMS-BH, …

Larp1 Haploinsufficiency Is Associated With An Autosomal Dominant Neurodevelopmental Disorder, James Chettle, Raymond J. Louie, Olivia Larner, Robert Best, Kevin Chen, Josephine Morris, Zinaida Dedeic, Roberta Sierra, Lori Berry, Kent Carter

School of Medicine Publications

Autism spectrum disorder (ASD) is a neurodevelopmental disorder (NDD) that affects approximately 4% of males and 1% of females in the United States. While causes of ASD are multi-factorial, single rare genetic variants contribute to around 20% of cases. Here we report a case series of seven unrelated probands (6 males, 1 female) with ASD or another variable NDD phenotype attributed to de novo heterozygous loss of function or missense variants in the gene LARP1. LARP1 encodes an RNA binding protein that post-transcriptionally regulates the stability and translation of thousands of mRNAs, including those regulating cellular metabolism and metabolic plasticity. …

The Internist's Post V.1 N.8, The University Of Texas Rio Grande Valley. School Of Medicine, Edgar Dorsey Trevino, Diana Othon Martinez, Ramon Elizondo Romo, Carlos Alejos Aguero, Elizabeth Mills-Reyes, Roque Mifuji, Martha Solis, Cesar Gutierrez

School of Medicine Publications

No abstract provided.

Mixed Methods Study Protocol: Language Identity, Discrimination, And Mental Health Among Multilingual 1.5 Generation Asian/Asian American Immigrant Young Adults, Chulwoo Park, Mark Edberg, Janet Yougi Bang, Avizia Yim Long

Faculty Research, Scholarly, and Creative Activity

Language identity, an understudied factor, can influence isolation and discrimination, leading to disparities in well-being and mental health among immigrants. This study aims to investigate the role of language identity on structural racism and discrimination among 1.5 generation Asian/Asian American immigrants in a diverse U.S. state. We developed a three-step sequential approach: Stage 1—qualitative analysis (1A, focus group discussion; 1B, in-depth interviews); Stage 2—quantitative analysis (2A, language identity measurement scale; 2B, cross-sectional online survey; 2C, multivariate multiple linear regression); Stage 3—another round of qualitative analysis (3A, follow-up in-depth chronological interviews). Therefore, this study will contribute to the field by introducing …

The Piper Survey. Ii. The Globular Cluster Systems Of Low Surface Brightness Galaxies In The Perseus Cluster, Steven R. Janssens, Duncan A. Forbes, Aaron J. Romanowsky, Jonah Gannon, Joel Pfeffer, Warrick J. Couch, Jean P. Brodie, William E. Harris, Patrick R. Durrell, Kenji Bekki

Faculty Research, Scholarly, and Creative Activity

We present Hubble Space Telescope ACS/WFC and WFC3/UVIS imaging for a sample of 50 low-surface brightness (LSB) galaxies in the ∼ 1015 M☉ Perseus cluster, which were originally identified in ground-based imaging. We measure the structural properties of these galaxies and estimate the total number of globular clusters (GCs) they host. Around half of our sample galaxies meet the strict definition of an ultra-diffuse galaxy (UDG), while the others are UDG-like but are either somewhat more compact or slightly brighter. A small number of galaxies reveal systems with many tens of GCs, rivalling some of the richest GC systems known …

Breakdown Of Boltzmann-Type Models For The Alignment Of Self-Propelled Rods, Patrick Murphy, Misha Perepelitsa, Ilya Timofeyev, Matan Lieber-Kotz, Brandon Islas, Oleg A. Igoshin

Faculty Research, Scholarly, and Creative Activity

Studies in the collective motility of organisms use a range of analytical approaches to formulate continuous kinetic models of collective dynamics from rules or equations describing agent interactions. However, the derivation of these kinetic models often relies on Boltzmann's “molecular chaos” hypothesis, which assumes that correlations between individuals are short-lived. While this assumption is often the simplest way to derive tractable models, it is often not valid in practice due to the high levels of cooperation and self-organization present in biological systems. In this work, we illustrated this point by considering a general Boltzmann-type kinetic model for the alignment of …

Principals' Perspectives Of The Impact Of Faculty Engagement, Self-Efficacy, And Resiliency On First-Year African American College Student Retention, Hattie Marie Jones

Electronic Theses and Dissertations

Abstract

This study examined principals’ perceptions of the impact of faculty engagement, student resiliency, and student self-efficacy on the retention of first-year urban and rural African American college students. The aim of the study was to determine why students from this demographic leave their higher education institutions after the first year. In the United States, about 30% of students, regardless of race or ethnicity, drop out of college after the first year. Further, given 6 years, about 50% of students drop out before obtaining a degree. Researchers have identified African American students as having a high college dropout rate. This …

The Relationship Of Acculturation With The Health Numeracy And Associated Health Behaviors Of Filipino-Americans, Ashwini Wagle, J. Cuaresma, Giselle A.P. Pignotti

Faculty Research, Scholarly, and Creative Activity

Describe relationships between acculturation level and the following variables - dietary acculturation and intake, health numeracy, physical activity, and anthropometric measurements - among Filipino-American men and women.

Self-Management, Attitudes, And Barriers For Students With Common Food Allergies Utilizing Campus Dining At A Large Urban University, Samantha Dahlberg, Ashwini Wagle, Jacqueline Bergman

Faculty Research, Scholarly, and Creative Activity

Food allergies are associated with stress and anxiety in college students. This research study aims to explore the findings of students with known food allergies and their perspectives on how one large urban university campus dining service accommodates their dietary needs. The study utilized a mixed-methods approach, and a non-probability, purposive sampling was used for a campus-wide online self-reported survey from August to October 2023. The survey included twenty close-ended and open-ended questions about the student’s food allergy attitudes, self-management, and barriers to on-campus dining services. Participants were students who self-identified with a medically diagnosed food allergy or intolerance and …

Unusual Metastatic Pathways: A Case Of Colorectal Adenocarcinoma Presenting As A Cervical Neck Mass, Taha Al Hassan, Jessica Flores, Adam Bender-Heine, Rachel A. Giese

School of Medicine Publications

Head and neck metastasis of colorectal adenocarcinoma is exceedingly rare with most cases presenting in the liver, lungs, or peritoneum. This report describes the case of a 53-year-old female patient with a past medical history significant for mucinous adenocarcinoma of the colon treated with a right hemicolectomy. She was thought to be in remission but presented a few years later with a new, isolated left cervical neck mass and symptoms of left eye ptosis and dryness. Diagnostic imaging and biopsy confirmed the neck mass to be a metastatic lesion from her prior mucinous adenocarcinoma, with immunohistochemical findings specific for colorectal …

Demystifying And Extracting Fault-Indicating Information From Logs For Failure Diagnosis, Junjie Huang, Zhihan Jiang, Jinyang Liu, Yintong Huo, Jiazhen Gu, Zhuangbin Chen, Cong Feng, Hui Dong, Zengyin Yang, Michael R. Lyu

Research Collection School Of Computing and Information Systems

Logs are imperative in the maintenance of online service systems, which often encompass important information for effective failure mitigation. While existing anomaly detection methodologies facilitate the identification of anomalous logs within extensive runtime data, manual investigation of log messages by engineers remains essential to comprehend faults, which is labor-intensive and error-prone. Upon examining the log-based troubleshooting practices at CloudA 1, we find that engineers typically prioritize two categories of log information for diagnosis. These include fault-indicating descriptions, which record abnormal system events, and fault-indicating parameters, which specify the associated entities. Motivated by this finding, we propose an approach to automatically …

Kpiroot: Efficient Monitoring Metric-Based Root Cause Localization In Large-Scale Cloud Systems, Wenwei Gu, Xinying Sun, Jinyang Liu, Yintong Huo, Zhuangbin Chen, Jianping Zhang, Jiazhen Gu, Yongqiang Yang, Michael R. Lyu

Research Collection School Of Computing and Information Systems

To ensure the reliability of cloud systems, their run-time status reflecting the service quality is periodically monitored with monitoring metrics, i.e., KPIs (key performance indicators). When performance issues happen, root cause localization pinpoints the specific KPIs that are responsible for the degradation of overall service quality, facilitating prompt problem diagnosis and resolution. To this end, existing methods generally locate root-cause KPIs by identifying the KPIs that exhibit a similar anomalous trend to the overall service performance. While straightforward, solely relying on the similarity calculation may be ineffective when dealing with cloud systems with complicated interdependent services. Recent deep learning-based methods …

Analysis Of Mybl1,Vxn, And Ccne2 Gene Relationships In Triple Negative Breast Cancer, Sahia M. Bryant

Theses (2016-Present)

Accounting for 15-20% of all breast cancers, triple-negative breast cancer (TNBC), is the most aggressive subtype, with the worst prognosis. In previous studies, the MYBL1 gene, which is associated with several events that are key to tumor progression, has been identified as a powerful transcriptional activator that is overexpressed in TNBC. In earlier research, our lab knocked down MYBL1 expression in a TNBC cell line and identified a subset of genes impacted by the knockdown process. MYBL1 gene is located on the chromosome 8q locus. In addition to MYBL1 we identified 2 genes, VXN and CCNE2, also located at the …

Investigation Of The Operational Benefits Of Flipped Left Diamond Interchange, Nazmus Salehin Asif,

Theses (2016-Present)

Interchange is an important element to accommodate the critical movement between arterials and freeways. To operate efficiently, innovative interchange designs have been suggested by transportation professionals. Recently, an innovative interchange design called flipped left diamond interchange (FLDI) design has been proposed. That aims to increase capacity and improve efficiency by flipping the left-turn lanes in opposing directions, eliminating conflicts between opposing left-turn movements. So, the signal timing of the left turn movements and through movements are independent which indicates the signal timing of these movements can be determined based on their volume. Due to this independence, any signal timing sequences …

Analysis Of Isoforms Associaated With The Mybl2 Gene In Triple Negative Breast Cancer, Taylor Allen-Boswell

Theses (2016-Present)

Nearly every gene exists as transcript variants and protein isoforms. Variations of a particular gene are generated by small nuclear ribonucleoproteins which in many cases remove introns, so that exons can be joined together in varying configurations. Transcript variants are formed, which are then translated into protein isoforms. The resulting transcript variants have substantial sequence similarities; and the isoforms have substantial sequence similarities. Studies show that isoforms generated because of these processes can have different start sites and/or sizes that can lead to generations of different proteins with different biological roles in a cell. The isoforms might have different functions …

Influenza C Virus In U.S. Children With Acute Respiratory Infection 2016-2019., Bethany K. Sederdahl, Geoffrey A. Weinberg, Angela P. Campbell, Rangaraj Selvarangan, Jennifer E. Schuster, Joana Y. Lively, Samantha M. Olson, Julie A. Boom, Pedro A. Piedra, Natasha B. Halasa, Laura Stewart, Peter G. Szilagyi, G K Balasubramani, Theresa Sax, Judith M. Martin, Robert W. Hickey, Marian G. Michaels, John V. Williams, New Vaccine Surveillance Network

Manuscripts, Articles, Book Chapters and Other Papers

Influenza C virus (ICV) is an orthomyxovirus related to influenza A and B, yet due to few commercial assays, epidemiologic studies may underestimate incidence of ICV infection and disease. We describe the epidemiology and characteristics of ICV within the New Vaccine Surveillance Network (NVSN), a Centers for Disease Control and Prevention (CDC)-led network that conducts population-based surveillance for pediatric acute respiratory illness (ARI). Nasal or/combined throat swabs were collected from emergency department (ED) or inpatient ARI cases, or healthy controls, between 12/05/2016-10/31/2019 and tested by molecular assays for ICV and other respiratory viruses. Parent surveys and chart review were used …

Clinical Pharmacogenetics Implementation Consortium Guideline (Cpic) For Cyp2d6, Adrb1, Adrb2, Adra2c, Grk4, And Grk5 Genotypes And Beta-Blocker Therapy., Julio D. Duarte, Cameron D. Thomas, Craig R. Lee, Rachel Huddart, Jose A G Agundez, Jordan F. Baye, Andrea Gaedigk, Teri E. Klein, David E. Lanfear, Andrew A. Monte, Mohamed Nagy, Matthias Schwab, C Michael Stein, Chakradhara Rao S. Uppugunduri, Ron H N Van Schaik, Roseann S. Donnelly, Kelly E. Caudle, Jasmine A. Luzum

Manuscripts, Articles, Book Chapters and Other Papers

Beta-blockers are widely used medications for a variety of indications, including heart failure, myocardial infarction, cardiac arrhythmias, and hypertension. Genetic variability in pharmacokinetic (e.g., CYP2D6) and pharmacodynamic (e.g., ADRB1, ADRB2, ADRA2C, GRK4, GRK5) genes have been studied in relation to beta-blocker exposure and response. We searched and summarized the strength of the evidence linking beta-blocker exposure and response with the six genes listed above. The level of evidence was high for associations between CYP2D6 genetic variation and both metoprolol exposure and heart rate response. Evidence indicates that CYP2D6 poor metabolizers experience clinically significant greater exposure and lower heart rate in …

Substance Use Emergency Department Visits Among Youths With Chronic Conditions During Covid-19., Faith Summersett Williams, Isabella Zaniletti, Abbey R. Masonbrink, Robert Garofalo, Maria Rahmandar, Niranjan S. Karnik, Geri Donenberg, Lisa Kuhns

Manuscripts, Articles, Book Chapters and Other Papers

IMPORTANCE: Pediatric emergency department (ED) visits for substance use (SU) increased during COVID-19. Better understanding of trends associated with SU ED visits among youths with a chronic medical condition (CMC) is needed to target SU screening, prevention, and intervention efforts in this population.

OBJECTIVE: To describe trends in pediatric SU ED visits before and during COVID-19 among youths in the US with and without CMCs and by race and ethnicity.

DESIGN, SETTING, AND PARTICIPANTS: In this cohort study, data were obtained from 47 US children's hospital EDs in the Pediatric Health Information System (PHIS) between March 1, 2018, and March …

Batchflex: Feature-Level Equalization Of X-Batch., Joshua T. Davis, Alyssa N. Obermayer, Alex C. Soupir, Rebecca S. Hesterberg, Thac Duong, Ching-Yao Yang, Ken Phong Dao, Brandon J. Manley, G Daniel Grass, Dorina Avram, Paulo C. Rodriguez, Brooke L. Fridley, Xiaoqing Yu, Mingxiang Teng, Xuefeng Wang, Timothy I. Shaw

Manuscripts, Articles, Book Chapters and Other Papers

MOTIVATION: Integrative analysis of heterogeneous expression data remains challenging due to variations in platform, RNA quality, sample processing, and other unknown technical effects. Selecting the approach for removing unwanted batch effects can be a time-consuming and tedious process, especially for more biologically focused investigators.

RESULTS: Here, we present BatchFLEX, a Shiny app that can facilitate visualization and correction of batch effects using several established methods. BatchFLEX can visualize the variance contribution of a factor before and after correction. As an example, we have analyzed ImmGen microarray data and enhanced its expression signals that distinguishes each immune cell type. Moreover, our …

Smooth Sigmoid Surrogate (Sss): An Alternative To Greedy Search In Decision Trees, Xiaogang Su, George E. Quaye, Yishu Wei, Joseph Kang, Lei Liu, Qiong Yang, Juanjuan Fan, Richard A. Levine

Manuscripts, Articles, Book Chapters and Other Papers

Greedy search (GS) or exhaustive search plays a crucial role in decision trees and their various extensions. We introduce an alternative splitting method called smooth sigmoid surrogate (SSS) in which the indicator threshold function used in GS is approximated by a smooth sigmoid function. This approach allows for parametric smoothing or regularization of the erratic and discrete GS process, making it more effective in identifying the true cutoff point, particularly in the presence of weak signals, as well as less prone to the inherent end-cut preference problem. Additionally, SSS provides a convenient means of evaluating the best split by referencing …

Evaluating The Efficacy Of And Preference For Interactive Computer Training With Student-Generated Examples, Sylvia C. Aquino, Stephanie Hood, Tara A. Fahmie, Richard Tanis

Psychology Faculty Research and Publications

Designing effective and preferred teaching practices for undergraduate students are common goals in behavior analytic training programs. A preliminary study by Nava et al. (2019) showed that undergraduate students generally rated peer-generated examples of the principles of behavior analysis as more preferred, relatable, and culturally responsive than traditional textbook examples. However, peer-generated examples did not result in any improvement in performance on concept knowledge assessments. The current study extended the study by Nava et al. by embedding peer-generated examples within interactive computer training (ICT) to provide opportunities for active responding, prompt fading, automated feedback, and practice with examples and nonexamples. …

Talar And Calcaneal Coordinate Axes Definitions Across Foot Pathologies, Kassidy Knutson, Erika P. Muhlrad, Andrew C. Peterson, Thomas Leonard, Abigail M. Anderson, Katelyn C. Aragon, Zachary J. Eatough, Bruce A. Macwilliams, Karen M. Kruger, Amy L. Lenz

Biomedical Engineering Faculty Research and Publications

The understanding of foot and ankle biomechanics is improving as new technology provides more detailed information about the motion of foot and ankle bones with biplane fluoroscopy, as well as the ability to analyze the hindfoot under weightbearing conditions with weightbearing computed tomography. Three-dimensional anatomical coordinate systems are necessary to describe the 3D alignment and kinematics of the foot and ankle. The lack of standard coordinate systems across research study sites can significantly alter experimental data analyses used for pre-surgical evaluation and post-operative outcome assessments. Clinical treatment paradigms are changing based on the expanding knowledge of complex pes planovalgus morphologies …

Phenotypes Of Velopharyngeal Tube Law In Obstructive Sleep Apnea, Devesh Kumar, B. Tucker Woodson, Guilherme J.M. Garcia

Biomedical Engineering Faculty Research and Publications

Objective

The biomechanics of upper airway collapse in obstructive sleep apnea (OSA) remains poorly understood. The goal of this study is to compare the area-pressure relationship (tube law) of the velopharynx at peak inspiration and peak expiration.

Study Design

Cross-sectional.

Setting

Academic tertiary medical center.

Methods

The velopharyngeal tube law was quantified in a convenience sample of 20 OSA patients via step reductions in nasal mask pressure during drug induced sleep endoscopy (DISE). The velopharyngeal airspace cross-sectional area was estimated from endoscopy while luminal pressure was recorded with a catheter. The tube law was quantified for nasal mask pressures from …

Editorial: Novel Computational Fluid Dynamics Methods For Diagnosis, Monitoring, Prediction, And Personalized Treatment For Cardiovascular Disease And Cancer Metastasis, Zahra Keshavarz Motamed, Nima Maftoon, Lakshmi Prasad Dasi, John F. Ladisa Jr.

Biomedical Engineering Faculty Research and Publications

No abstract provided.

A Content Analysis Of Counseling Psychology Literature: Resilience Against Oppression Among People Of Color, David C. Stanley Jr., Rawan H. Atari-Khan

Psychology Faculty Research and Publications

The researchers analyzed articles from two flagship counseling psychology journals (i.e., Journal of Counseling Psychology and The Counseling Psychologist) to examine current understandings of resilience. There were 54 articles included in the final analysis that spanned the years 1997–2022. The researchers conducted a content analysis to identify, analyze, and report patterns across counseling psychology journals with regard to how resilience has been defined, the racial/ethnic groups that were of focus, and the forms of oppression that were studied or addressed. Five themes were generated that are a direct representation of the topics within previous literature on resilience in the field …

Examining Factors Affecting The Implementation Of Restorative Practices In Elementary Schools: Supporting And Challenging Aspects For Principals, Salma Hussein

School of Education and Leadership Student Capstone Theses and Dissertations

This qualitative research seeks to gather information that will be useful for successfully implementing Restorative Practices from Minnesota elementary school principals. Elementary Principals have been interviewed to share their experiences with implementing Restorative Practices. It specifically focuses on identifying the successes and challenges, particularly in efforts to reduce racial disparities in discipline data.The study also examines how principals apply these practices in their elementary schools to create caring communities. Restorative Practices have emerged as more schools and states move towards non exclusionary discipline practices to better support students and build caring school communities. This research seeks to provide insights into …

Effective Practices For Dual-Identified English Learners In Special Education Using A Quantitative Secondary Data Analysis Of Access For Ells Testing Results And Qualitative Case Studies, Brett Frayseth

School of Education and Leadership Student Capstone Theses and Dissertations

A student dual-identified to receive English learning and special education services is legally entitled to receive both services. Although there are recommendations for how to provide these services, there is little evidence of what has demonstrated success, despite there being schools which have been able to create such programs. This mixed methods research focused on identifying schools in Minnesota that successfully provided measurable growth in their dual-identified student population. Data were gathered from educators in those schools to understand how they found this success for their dual-identitfied students. This research began with a quantitative secondary data analysis of ACCESS for …

"Servant Leadership: Perceptions And Practices Of Parochial School Administrators In The K-12 Setting ", Craig Swanson

School of Education and Leadership Student Capstone Theses and Dissertations

This study addressed the dichotomy between administrators' perceptions of themselves as servant leaders and their implementation of servant leadership practices in parochial schools. Although servant leadership aligns with parochial school values, simply adopting the terminology without true implementation can undermine school effectiveness. The purpose of this qualitative case study was to examine whether differences exist between administrators' perceptions of their servant leadership and teachers' perceptions of how administrators implement servant leadership practices. The study employed a phenomenological case study approach using the Servant Leadership Questionnaire (SLQ) and administrator interviews. Three administrators and ten teachers from two Christian K-12 schools in …

Vicarious Trauma Of Adult Tesol Educators: A Brief Investigation Of Screening Methods, Kenzie Howden

School of Education and Leadership Student Capstone Theses and Dissertations

This study explored the question: How do Adult Education and Literacy Program teachers in the Teaching English to Speakers of Other Languages context describe their experiences with teacher vicarious trauma, and does a commonly used screening tool show similar levels of teacher vicarious trauma?. Social science research has used the Professional Quality of Life (ProQOL; Stamm, 2010), a quantitative screening tool to explain vicarious trauma and related measures, and these methods have been recently adopted in research in adult education settings (Hickey et al., 2020). This study used a mixed methods approach, with 10 Adult Education and Literacy Program teachers …