Medicine and Health Sciences Commons^™

Advanced Prognostic Modeling For Breast Cancer Patients: Leveraging Data-Driven Approaches For Survival Analysis, Theophilus Gyedu Baidoo

Theses and Dissertations

Breast cancer is the second most prevalent form of cancer in women in the United States. Each year, about 264,000 cases of breast cancer are diagnosed in women and of this number, about 42,000 women lose their lives as reported by the Centers for Disease Control and Prevention. Early detection and effective treatment are crucial for improving survival rates and reducing mortality. This study aimed to explore the influential factors that may risk the survival of women with the disease and compare their predictive abilities using several error and performance metrics. The study uses a dataset from the National Cancer …

Fast Inference Of Genetic Recombination Rates In Biobank Scale Data, Ardalan Naseri, William Yue, Shaojie Zhang, Degui Zhi

Faculty, Staff and Student Publications

Although rates of recombination events across the genome (genetic maps) are fundamental to genetic research, the majority of current studies only use one standard map. There is evidence suggesting population differences in genetic maps, and thus estimating population-specific maps, are of interest. Although the recent availability of biobank-scale data offers such opportunities, current methods are not efficient at leveraging very large sample sizes. The most accurate methods are still linkage disequilibrium (LD)-based methods that are only tractable for a few hundred samples. In this work, we propose a fast and memory-efficient method for estimating genetic maps from population genotyping data. …

Multi-Task Learning With Dynamic Re-Weighting To Achieve Fairness In Healthcare Predictive Modeling, Can Li, Sirui Ding, Na Zou, Xia Hu, Xiaoqian Jiang, Kai Zhang

Faculty, Staff and Student Publications

The emphasis on fairness in predictive healthcare modeling has increased in popularity as an approach for overcoming biases in automated decision-making systems. The aim is to guarantee that sensitive characteristics like gender, race, and ethnicity do not influence prediction outputs. Numerous algorithmic strategies have been proposed to reduce bias in prediction results, mitigate prejudice toward minority groups and promote prediction fairness. The goal of these strategies is to ensure that model prediction performance does not exhibit significant disparity among sensitive groups. In this study, we propose a novel fairness-achieving scheme based on multitask learning, which fundamentally differs from conventional fairness-achieving …

Weakly Supervised Spatial Relation Extraction From Radiology Reports, Surabhi Datta, Kirk Roberts

Faculty, Staff and Student Publications

OBJECTIVE: Weak supervision holds significant promise to improve clinical natural language processing by leveraging domain resources and expertise instead of large manually annotated datasets alone. Here, our objective is to evaluate a weak supervision approach to extract spatial information from radiology reports.

MATERIALS AND METHODS: Our weak supervision approach is based on data programming that uses rules (or labeling functions) relying on domain-specific dictionaries and radiology language characteristics to generate weak labels. The labels correspond to different spatial relations that are critical to understanding radiology reports. These weak labels are then used to fine-tune a pretrained Bidirectional Encoder Representations from …

Minimal Positional Substring Cover Is A Haplotype Threading Alternative To Li And Stephens Model, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang

Faculty, Staff and Student Publications

The Li and Stephens (LS) hidden Markov model (HMM) models the process of reconstructing a haplotype as a mosaic copy of haplotypes in a reference panel. For small panels, the probabilistic parameterization of LS enables modeling the uncertainties of such mosaics. However, LS becomes inefficient when sample size is large, because of its linear time complexity. Recently the PBWT, an efficient data structure capturing the local haplotype matching among haplotypes, was proposed to offer a fast method for giving some optimal solution (Viterbi) to the LS HMM. Previously, we introduced the minimal positional substring cover (MPSC) problem as an alternative …

A Comparative Effectiveness Study On Opioid Use Disorder Prediction Using Artificial Intelligence And Existing Risk Models, Sajjad Fouladvand, Jeffery Talbert, Linda Phyliss Dwoskin, Heather M. Bush, Amy L. Meadows, Lars E. Peterson, Yash R. Mishra, Steven K. Roggenkamp, Fei Wang, Ramakanth Kavuluru, Jin Chen

Markey Cancer Center Faculty Publications

Opioid use disorder (OUD) is a leading cause of death in the United States placing a tremendous burden on patients, their families, and health care systems. Artificial intelligence (AI) can be harnessed with available healthcare data to produce automated OUD prediction tools. In this retrospective study, we developed AI based models for OUD prediction and showed that AI can predict OUD more effectively than existing clinical tools including the unweighted opioid risk tool (ORT). Data include 474,208 patients’ data over 10 years; 269,748 were females with an average age of 56.78 years. Cases are prescription opioid users with at least …

The Metabolomics Workbench File Status Website: A Metadata Repository Promoting Fair Principles Of Metabolomics Data, Christian D. Powell, Hunter N. B. Moseley

Markey Cancer Center Faculty Publications

Background: An updated version of the mwtab Python package for programmatic access to the Metabolomics Workbench (MetabolomicsWB) data repository was released at the beginning of 2021. Along with updating the package to match the changes to MetabolomicsWB’s ‘mwTab’ file format specification and enhancing the package’s functionality, the included validation facilities were used to detect and catalog file inconsistencies and errors across all publicly available datasets in MetabolomicsWB.

Results: The MetabolomicsWB File Status website was developed to provide continuous validation of MetabolomicsWB data files and a useful interface to all found inconsistencies and errors. This list of detectable issues/errors include format …

Amyloid-Beta Protein Concentration Dependence Of Reversible Aggregation Using Gold Colloid Particles, Renee Spencer, Lila Kocieniewski, Bryan Martinez, Kazushige Yokoyama

McNair Scholars Program

Although Alzheimer’s and COVID-19 are different diseases, the commonality between them is during the process of them developing in a person by fibrillogenesis. The product of fibrillogenesis results in the development of these diseases. We study the first stage of fibrillogenesis where the amyloid-beta peptide monomers are assembled into an oligomer. We want to isolate this oligomer using gold colloids because this step can be reversed. Utilizing gold colloids allows us to freeze fibrillogenesis in the first step by folding and unfolding the protein repeatedly through a series of pH changes from 4 or below to 10 or higher. At …

Singapore's Hospital To Home Program: Raising Patient Engagement Through Ai, John Abisheganaden, Kheng Hock Lee, Lian Leng Low, Eugene Shum, Han Leong Goh, Christine Gian Lee Ang, Andy Wee An Ta, Steven M. Miller

Research Collection School Of Computing and Information Systems

Because of their complex care needs, many elderly patients are discharged from hospitals only to be readmitted for multiple stays within the following twelve months. John Abisheganaden and his fellow authors describe Singapore’s Hospital to Home program, a community care initiative fueled by artificial intelligence.

Balancing Privacy And Flexibility Of Cloud-Based Personal Health Records Sharing System, Yudi Zhang, Fuchun Guo, Willy Susilo, Guomin Yang

Research Collection School Of Computing and Information Systems

The Internet of Things and cloud services have been widely adopted in many applications, and personal health records (PHR) can provide tailored medical care. The PHR data is usually stored on cloud servers for sharing. Weighted attribute-based encryption (ABE) is a practical and flexible technique to protect PHR data. Under a weighted ABE policy, the data user's attributes will be “scored”, if and only if the score reaches the threshold value, he/she can access the data. However, while this approach offers a flexible access policy, the data owners have difficulty controlling their privacy, especially sharing PHR data in collaborative e-health …

Institute For Global Health And Development : Issue 5 - July 2023, Institute For Global Health And Development

IGHD Newsletters

• Research Highlights
• Key Publications
• IGHD in the News
• Webinars, Academics & Conferences
• ‘Choice’ Programme - Technical Advisory Group
• Welcome New Team Members
• Mark your Calendars: Upcoming Event
• Congratulations Team IGHD
• Collaborate With Us

Empowering Patient Similarity Networks Through Innovative Data-Quality-Aware Federated Profiling, Alramzana Nujum Navaz, Mohamed Adel Serhani, Hadeel T. El Kassabi, Ikbal Taleb

All Works

Continuous monitoring of patients involves collecting and analyzing sensory data from a multitude of sources. To overcome communication overhead, ensure data privacy and security, reduce data loss, and maintain efficient resource usage, the processing and analytics are moved close to where the data are located (e.g., the edge). However, data quality (DQ) can be degraded because of imprecise or malfunctioning sensors, dynamic changes in the environment, transmission failures, or delays. Therefore, it is crucial to keep an eye on data quality and spot problems as quickly as possible, so that they do not mislead clinical judgments and lead to the …

Meet Me In The Middle: A Scoping Review On Understanding Adolescent Needs In Climate Communication, Gwendolyn Monica Hoff Anderson

Master's Projects and Capstones

The greatest effects of climate change are likely to be felt by youth. Young people are disproportionately affected by climate change due to their critical developmental stage and lack of power, and they experience both higher severity and prevalence of mental health issues related to climate change. Strong emotions have long been recognized as potential catalysts for action, or they may lead to paralyzing feelings of being overwhelmed. Climate communication is a critical tool to spark climate concern and encourage action. Activism, in turn, may help youth manage their anxiety about climate change. This scoping review examines emerging evidence on …

Privacy Preserving Identification Of Population Stratification For Collaborative Genomic Research, Leonard Dervishi, Wenbiao Li, Anisa Halimi, Xiaoqian Jiang, Jaideep Vaidya, Erman Ayday

Faculty, Staff and Student Publications

The rapid improvements in genomic sequencing technology have led to the proliferation of locally collected genomic datasets. Given the sensitivity of genomic data, it is crucial to conduct collaborative studies while preserving the privacy of the individuals. However, before starting any collaborative research effort, the quality of the data needs to be assessed. One of the essential steps of the quality control process is population stratification: identifying the presence of genetic difference in individuals due to subpopulations. One of the common methods used to group genomes of individuals based on ancestry is principal component analysis (PCA). In this article, we …

Monitoring Personal Exposure To Air Quality Gradients While Biking On An Elevated Urban Trail, Gavin D. Salas

DePaul Discoveries

Air pollution is a major global health concern, specifically as it relates to the human exposome. The EPA criteria pollutants, including particulate matter (PM), carbon monoxide (CO), carbon dioxide (CO₂), and NO_x can have severe impacts on respiratory and cardiovascular health, particularly in populations with chronic illnesses such as asthma, those facing economic hardships and individuals who frequently spend time outdoors, such as bicyclists and runners. To understand the impact of air pollution on human health, it is essential to assess personal exposure. This study aimed to investigate personal exposure to air pollution levels while biking along …

Depaul Discoveries Volume 12 Cover Art, Katherine Petralia

DePaul Discoveries

No abstract provided.

Instrument Building For Detection Of Triplet Signal From Quinolinone Molecules, Brooke Weitzel

DePaul Discoveries

Conjugated organic molecules such as the 2-quinolinone family can be used as energy-donor molecules in photocatalysis because of their light absorbing and energy transmitting qualities. Good donor molecules have triplet excited states that are useful for photocatalysis due to their long lifetimes. The goal of this research was to build a near-infrared emission spectroscopy instrument to observe a triplet signal in a set of five previously synthesized 2-quinolinone molecules. A near-infrared absorbance instrument was built successfully with accurate measurements; however, there was no detection of the desired triplet emission signal.

The Influence Of Vehicular Traffic And Land Use Typology On The Spatial Patterns And Concentrations Of Soil Lead (Pb) In The Uptown Community Area Of Chicago, Andreas 'Dre' Harris

DePaul Discoveries

Lead (Pb) is a harmful element whose presence threatens the well-being of living organisms and their environments. There are higher concentrations and an increased risk of Pb exposure in areas that provide fewer natural pathways for Pb to accumulate into. In urban areas, the soil is one of the most common and available environmental sinks for Pb accumulation. This study examines the total soil Pb concentrations in relation to land-use types and average daily traffic volumes (cars/day) in each census tract in the Uptown Community Area of Chicago. This study provides insight into how land use and traffic volume may …

Acquisition Of A Lexicon For Family History Information: Bidirectional Encoder Representations From Transformers-Assisted Sublanguage Analysis, Liwei Wang, Huan He, Andrew Wen, Sungrim Moon, Sunyang Fu, Kevin J Peterson, Xuguang Ai, Sijia Liu, Ramakanth Kavuluru, Hongfang Liu

Faculty, Staff and Student Publications

BACKGROUND: A patient's family history (FH) information significantly influences downstream clinical care. Despite this importance, there is no standardized method to capture FH information in electronic health records and a substantial portion of FH information is frequently embedded in clinical notes. This renders FH information difficult to use in downstream data analytics or clinical decision support applications. To address this issue, a natural language processing system capable of extracting and normalizing FH information can be used.

OBJECTIVE: In this study, we aimed to construct an FH lexical resource for information extraction and normalization.

METHODS: We exploited a transformer-based method to …

Using Ai-Generated Suggestions From Chatgpt To Optimize Clinical Decision Support, Siru Liu, Aileen P Wright, Barron L Patterson, Jonathan P Wanderer, Robert W Turer, Scott D Nelson, Allison B Mccoy, Dean F Sittig, Adam Wright

Faculty, Staff and Student Publications

OBJECTIVE: To determine if ChatGPT can generate useful suggestions for improving clinical decision support (CDS) logic and to assess noninferiority compared to human-generated suggestions.

METHODS: We supplied summaries of CDS logic to ChatGPT, an artificial intelligence (AI) tool for question answering that uses a large language model, and asked it to generate suggestions. We asked human clinician reviewers to review the AI-generated suggestions as well as human-generated suggestions for improving the same CDS alerts, and rate the suggestions for their usefulness, acceptance, relevance, understanding, workflow, bias, inversion, and redundancy.

RESULTS: Five clinicians analyzed 36 AI-generated suggestions and 29 human-generated suggestions …

Trend Observation: Analysis On Development Trend Of Precision Medicine

Bulletin of Chinese Academy of Sciences (Chinese Version)

No abstract provided.

Atomistic Assessment Of Drug-Phospholipid Interactions Consequent To Cancer Treatment: A Study Of Anthracycline Cardiotoxicity, Yara Elsayed Ahmed

Theses and Dissertations

Despite being one of the most effective chemotherapeutic agents developed to date, Anthracyclines are notorious for their cardiotoxicity. Their clinical use is frequently limited both in dosage and in prescription due to the severe cardiac damage they cause. The mechanism of anthracycline-induced cardiotoxicity is not yet fully understood. However, it is hypothesized that interactions with the myocardial membrane play an important role in imparting cardiotoxicity. In this study, we use molecular dynamics simulations and density functional theory calculations to study the anthracycline drug molecules and the interactions that they have with the myocardial membrane. We construct a myocardial membrane model …

Optical Characterisation Of Holographic Diffusers And Bangerter Foils For Treatment Of Amblyopia, Matthew Hellis, Suzanne Martin, Matthew Sheehan, Kevin Murphy

Articles

Amblyopia is a significant issue for children worldwide, and current treatment methods have drawbacks that can hinder treatment effectiveness and/or patient experience. This study proposes a new treatment method using holographic diffusers while also comparing their optical characteristics to a current treatment method (Bangerter foils). Holographic diffusers were developed by optically patterning thin polymer layers on a micron scale. Two compositions of photopolymer (acrylamide and diacetone acrylamide based) are analysed herein. Characterisation shows that holographic diffusers of either composition can achieve a wide range of on-axis intensity reductions, allowing for precise and customisable treatment levels by altering recording exposure time …

Exposure Levels Of Airborne Fungi, Bacteria, And Antibiotic Resistance Genes In Cotton Farms During Cotton Harvesting And Evaluations Of N95 Respirators Against These Bioaerosols, Atin Adhikari, Pratik Banerjee, Taylor Thornton, Daleniece Higgins, Caleb Adeoye, Sonam Sherpa

Biostatistics, Epidemiology & Environmental Health Sciences: Faculty Publications

The USA is the third-leading cotton-producing country worldwide and cotton farming is common in the state of Georgia. Cotton harvest can be a significant contributor to airborne microbial exposures to farmers and nearby rural communities. The use of respirators or masks is one of the viable options for reducing organic dust and bioaerosol exposures among farmers. Unfortunately, the OSHA Respiratory Protection Standard (29 CFR Part 1910.134) does not apply to agricultural workplaces and the filtration efficiency of N95 respirators was never field-tested against airborne microorganisms and antibiotic resistance genes (ARGs) during cotton harvesting. This study addressed these two information gaps. …

Preliminary Evidence Of Anticoagulant Rodenticide Exposure In American Kestrels (Falco Sparverius) In The Western United States, Evan R. Buechley, Dave Oleyar, Jesse L. Watson, Jennifer Bridgeman, Steven Volker, David A. Goldade, Catherine E. Swift, Barnett A. Rattner

United States Geological Survey: Staff Publications

Although there is extensive evidence of declines in the American Kestrel (Falco sparverius) population across North America, the cause of such declines remains a mystery. One hypothesized driver of decline is anticoagulant rodenticide (AR) exposure, which could potentially cause mortality or reduced fitness. We investigated AR exposure in wild American Kestrels in Utah, USA. We collected and tested for AR residues in liver samples (n = 8) from kestrels opportunistically encountered dead and in blood samples (n = 71) from live wild kestrels, both nestlings and adults. We found high detection rates in both tissues. Adult …

Childhood Asthma-Management Practices In Rural Nigeria: Exploring The Knowledge, Attitude, And Practice Of Caregivers In Oyo State, Oyindamola Akinso, Atin Adhikari, Jingjing Yin, Joanne Chopak-Foss, Gulzar H. Shah

Biostatistics, Epidemiology & Environmental Health Sciences: Faculty Publications

Background: Caregivers of asthmatic children have a poor knowledge of proper asthma-management practices in Nigeria. This study examined the knowledge, attitudes, and practice behaviors of caregivers in the management of asthma in children under 5 years of age in Oyo State, Nigeria. Methods: While a mixed method was used in the original research, this brief describes the quantitative method used in this study to evaluate caregivers’ asthma-management practices. A 55-item questionnaire on childhood asthma knowledge, attitude, and practice was administered during child welfare-clinic visits to 118 caregivers. Data were analyzed using the IBM SPSS Version 25.0. Statistical significance was set …

A Nurse-Led Telehealth Program For Diabetes Foot Care: Feasibility And Usability Study, Hsiao-Hui Ju, Rashmi Momin, Stanley Cron, Jed Jularbal, Jeffery Alford, Constance Johnson

Faculty, Staff and Student Publications

BACKGROUND: Diabetes mellitus can lead to severe and debilitating foot complications, such as infections, ulcerations, and amputations. Despite substantial progress in diabetes care, foot disease remains a major challenge in managing this chronic condition that causes serious health complications worldwide.

OBJECTIVE: The primary aim of this study was to examine the feasibility and usability of a telehealth program focused on preventive diabetes foot care. A secondary aim was to descriptively measure self-reported changes in diabetes knowledge, self-care, and foot care behaviors before and after participating in the program.

METHODS: The study used a single-arm, pre-post design in 2 large family …

Variant Spectrum Of Von Hippel-Lindau Disease And Its Genomic Heterogeneity In Japan, Kenji Tamura, Yuki Kanazashi, Chiaki Kawada, Yuya Sekine, Kazuhiro Maejima, Shingo Ashida, Takashi Karashima, Shohei Kojima, Nickolas F Parrish, Shunichi Kosugi, Chikashi Terao, Shota Sasagawa, Masashi Fujita, Todd A Johnson, Yukihide Momozawa, Keiji Inoue, Taro Shuin, Hidewaki Nakagawa

Faculty, Staff and Student Publications

Von Hippel-Lindau (VHL) disease is an autosomal dominant, inherited syndrome with variants in the VHL gene, causing predisposition to multi-organ neoplasms with vessel abnormality. Germline variants in VHL can be detected in 80-90% of patients clinically diagnosed with VHL disease. Here, we summarize the results of genetic tests for 206 Japanese VHL families, and elucidate the molecular mechanisms of VHL disease, especially in variant-negative unsolved cases. Of the 206 families, genetic diagnosis was positive in 175 families (85%), including 134 families (65%) diagnosed by exon sequencing (15 novel variants) and 41 (20%) diagnosed by multiplex ligation-dependent probe amplification (MLPA) (one …

Mitotrace: A Computational Framework For Analyzing Mitochondrial Variation In Single-Cell Rna Sequencing Data, Mingqiang Wang, Wankun Deng, David C Samuels, Zhongming Zhao, Lukas M Simon

Faculty, Staff and Student Publications

Genetic variation in the mitochondrial genome is linked to important biological functions and various human diseases. Recent progress in single-cell genomics has established single-cell RNA sequencing (scRNAseq) as a popular and powerful technique to profile transcriptomics at the cellular level. While most studies focus on deciphering gene expression, polymorphisms including mitochondrial variants can also be readily inferred from scRNAseq. However, limited attention has been paid to investigate the single-cell landscape of mitochondrial variants, despite the rapid accumulation of scRNAseq data in the community. In addition, a diploid context is assumed for most variant calling tools, which is not appropriate for …

Digital Health Technologies For Peripartum Depression Management Among Low-Socioeconomic Populations: Perspectives From Patients, Providers, And Social Media Channels, Alexandra Zingg, Tavleen Singh, Amy Franklin, Angela Ross, Sudhakar Selvaraj, Jerrie Refuerzo, Sahiti Myneni

Faculty, Staff and Student Publications

BACKGROUND: Peripartum Depression (PPD) affects approximately 10-15% of perinatal women in the U.S., with those of low socioeconomic status (low-SES) more likely to develop symptoms. Multilevel treatment barriers including social stigma and not having appropriate access to mental health resources have played a major role in PPD-related disparities. Emerging advances in digital technologies and analytics provide opportunities to identify and address access barriers, knowledge gaps, and engagement issues. However, most market solutions for PPD prevention and management are produced generically without considering the specialized needs of low-SES populations. In this study, we examine and portray the information and technology needs …