Digital Commons Network^™

Supervised Classification Modeling On Louisiana Medicaid Data: A Comparative Study, Yead Rahman

Master's Theses

This thesis systematically optimizes and compares state-of-the-art supervised classification models for Louisiana Medicaid data targeting clinical services, COVID-19 infection, and tobacco use. These target variables are critically important as they represent key health outcomes and behaviors among Medicaid enrollees in Louisiana, a population often characterized by poverty and limited access to education. This study applies advanced machine learning techniques to identify the best model for multinomial and binary classification tasks. These include models such as Logistic Regression, XGBoost, AdaBoost, Random Forest, Decision Tree, Artificial Neural Networks, and Naïve Bayes. Extensive tuning of the hyperparameters and optimization of each classifier were …

Developing A Comprehensive Cognitive Model Of Math Achievement, Nina Anderson

Electronic Theses and Dissertations

Recently, downward trends have been reported in U.S. children’s math performance following school disruptions during COVID-19 amidst longstanding concerns for instruction and curricula within the subject. In support of efforts to remedy these declines, the current work presents two studies dedicated to identifying cognitive factors that are most strongly related to math performance, and which therefore offer promising potential targets for assessment and intervention. Both studies use data from the Colorado Learning Disabilities Research Center, which includes participants ages 8 - 16 and multiple well-validated measures of all constructs of interest. Study 1 tests three alternative latent cognitive models of …

Slow Ramping Emerges From Spontaneous Fluctuations In Spiking Neural Networks, Jake Gavenas, Ueli Rutishauer, Aaron Schurger, Uri Maoz

Psychology Faculty Articles and Research

The capacity to initiate actions endogenously is critical for goal-directed behavior. Spontaneous voluntary actions are typically preceded by slow-ramping activity in medial frontal cortex that begins around two seconds before movement, which may reflect spontaneous fluctuations that influence action timing. However, the mechanisms by which these slow ramping signals emerge from single-neuron and network dynamics remain poorly understood. Here, we developed a spiking neural-network model that produces spontaneous slow ramping activity in single neurons and population activity with onsets ~2 s before threshold crossings. A key prediction of our model is that neurons that ramp together have correlated firing patterns …

Metabolite Biomarker Discovery For Lung Cancer Using Machine Learning, Ariski Fajarido, Linda Erlina, Aryo Tedjo, Fadilah Fadilah, Wawaimuli Arozal

Indonesian Journal of Medical Chemistry and Bioinformatics

Lung cancer is the leading cause of cancer death worldwide. About 2.1 million lung cancer patients were diagnosed in 2018, accounting for about 11.6% of all newly diagnosed cancer cases. For lung cancer, blood is the first choice as a source of screening biomarker candidates. Blood biomarkers provide a snapshot of the patient's entire body, including the primary tumor, metastatic disease, immune response, and peritumoral stroma. However, sputum sampling, bronchial lavage or aspiration, exhaled breath (EB), and airway epithelial sampling represent unique samples for lung cancer and other airway cancers as potential sources for alternative biomarkers. Metabolites are products of …

Exploration Of Positive Deviance In Prevention Of Underweight In The Under-Five: A Qualitative Study On Low-Income Urban Families, Irwan Budiono, Lukman Fauzi, Dewi Sari Rochmayani

Kesmas

Children under the age of five (the under-five) from low-income families are more vulnerable to experience underweight. This nutritional vulnerability is evident in the preliminary study, where 35.1% of the under-five experience underweight, and 28.48% are low-income families. This study aimed to explore Positive Deviance (PD) behaviors in preventing underweight among the under-five. The study applied a qualitative approach with a case study design. Data collection took place in July-August 2022, focusing on low-income families in the Gunung Brintik area. Data were collected through two focus group discussions, seven in-depth interviews, and five key informant interviews. Coding, subtheme, and theme …

Risk Factors For Cognitive Impairment In Adult Population Of Coastal Area: A Cross-Sectional Study In Maringkik Island, Indonesia, Herpan Syafii Harahap, Arina Windri Rivarti, Nurhidayati Nurhidayati, Fitriannisa Faradina Zubaidi, Dini Suryani, Legis Ocktaviana Saputri, Yanna Indrayana, Athalita Andhera, Muhammad Hilam, Abiyyu Didar Haq

Kesmas

Cognitive impairment is a medical condition commonly found in elderly populations, which can be due to vascular risk factors in patients. There remains limited data on risk factors for cognitive impairment among coastal region populations. This study aimed to investigate risk factors for cognitive impairment in the adult population of Maringkik Island, West Nusa Tenggara Province, Indonesia. Data collected were age, sex, education level, hypertension, antihypertensive treatment, diabetes mellitus, cigarette smoking, and body mass index status. A total of 114 participants were recruited using a consecutive sampling method. The participants’ cognitive function assessment used the Mini-Cog instrument. The cognitive impairment …

Variation And Predictors Of Covid-19 Mortality In Hospitalized Cases In West Sumatra Province, Indonesia: A Retrospective Observational Study, Defriman Djafri, Ade Suzana Eka Putri, Yudi Pradipta

Kesmas

During 2020, the year of the COVID-19 pandemic, different Indonesian provinces had different numbers of COVID-19 infections and fatalities, particularly in West Sumatra Province. This study aimed to investigate the variation of confirmed COVID-19 cases and determine predictors of mortality in hospitalized patients across districts in West Sumatra Province. A retrospective observational study was conducted during the COVID-19 pandemic. From March 2020 to June 2021, 46,005 confirmed cases were collected in the province, of which 42,308 were hospitalized and analyzed. Confirmed cases and deaths were compared by geographic location using spatial analysis. The risk predictors of death were estimated using …

Therapeutic Antisense Oligonucleotides In Oncology: From Bench To Bedside, Elif Çakan, Olivia D Lara, Anna Szymanowska, Emine Bayraktar, Arturo Chavez-Reyes, Paola Amero

Faculty, Staff and Student Publications

Advancements in our comprehension of tumor biology and chemoresistance have spurred the development of treatments that precisely target specific molecules within the body. Despite the expanding landscape of therapeutic options, there persists a demand for innovative approaches to address unmet clinical needs. RNA therapeutics have emerged as a promising frontier in this realm, offering novel avenues for intervention such as RNA interference and the utilization of antisense oligonucleotides (ASOs). ASOs represent a versatile class of therapeutics capable of selectively targeting messenger RNAs (mRNAs) and silencing disease-associated proteins, thereby disrupting pathogenic processes at the molecular level. Recent advancements in chemical modification …

Perceptions Of Hiv-Related Comorbidities And Usability Of A Virtual Environment For Cardiovascular Disease Prevention Education In Sexual Minority Men With Hiv: Formative Phases Of A Pilot Randomized Controlled Trial, Trace Kershaw, Julian F Thayer, Allison Vorderstrasse

Faculty, Staff and Student Publications

Background: Sexual minority men with HIV are at an increased risk of cardiovascular disease (CVD) and have been underrepresented in behavioral research and clinical trials.

Objective: This study aims to explore perceptions of HIV-related comorbidities and assess the interest in and usability of a virtual environment for CVD prevention education in Black and Latinx sexual minority men with HIV.

Methods: This is a 3-phase pilot behavioral randomized controlled trial. We report on formative phases 1 and 2 that informed virtual environment content and features using qualitative interviews, usability testing, and beta testing with a total of 25 individuals. In phase …

Sexannodb, A Knowledgebase Of Sex-Specific Regulations From Multi-Omics Data Of Human Cancers, Sijia Wu, Weiling Zhao, Pora Kim, Xiaobo Zhou

Faculty, Staff and Student Publications

Background

Sexual differences across molecular levels profoundly impact cancer biology and outcomes. Patient gender significantly influences drug responses, with divergent reactions between men and women to the same drugs. Despite databases on sex differences in human tissues, understanding regulations of sex disparities in cancer is limited. These resources lack detailed mechanistic studies on sex-biased molecules.

Methods

In this study, we conducted a comprehensive examination of molecular distinctions and regulatory networks across 27 cancer types, delving into sex-biased effects. Our analyses encompassed sex-biased competitive endogenous RNA networks, regulatory networks involving sex-biased RNA binding protein-exon skipping events, sex-biased transcription factor-gene regulatory networks, …

Epigenome-Wide Association Study Of Prostate Cancer In African American Men Identified Differentially Methylated Genes, Anders Berglund, Kosj Yamoah, Steven A. Eschrich, Rana Falahat, James J. Mulé, Sungjune Kim, Jaime Matta, Julie Dutil, Gilberto Ruiz-Deya, Carmen Ortiz Sanchez, Liang Wang, Hyun Park, Hirendra N. Banerjee, Tamara Lotan, Kathryn Hughes Barry, Ryan M. Putney, Seung Joon Kim, Clement Gwede, Jacob K. Kresovich, Youngchul Kim, Hui Yi Lin, Jasreman Dhillon, Ratna Chakrabarti, Jong Y. Park

School of Public Health Faculty Publications

Introduction: Men with African ancestry have the highest incidence and mortality rates of prostate cancer (PCa) worldwide. Methods: This study aimed to identify differentially methylated genes between tumor vs. adjacent normal and aggressive vs. indolent PCa in 121 African American patients. Epigenome-wide DNA methylation patterns in tumor DNA were assessed using the human Illumina Methylation EPIC V1 array. Results: Around 5,139 differentially methylated CpG-sites (q < 0.01, lΔβl > 0.2) were identified when comparing normal vs. tumor, with an overall trend of hypermethylation in prostate tumors. Multiple representative differentially methylated regions (DMRs), including immune-related genes, such as CD40, Galectin3, OX40L, and STING, were detected …

Analysis Of Serum Exosome Metabolites Identifies Potential Biomarkers For Human Hepatocellular Carcinoma, Li Song, Didi Xing, Hui Li

Faculty, Staff and Student Publications

Currently, the clinical cure rate for primary liver cancer remains low. Effective screening and early diagnosis of hepatocellular carcinoma (HCC) remain clinical challenges. Exosomes are intimately associated with tumor development and their contents have the potential to serve as highly sensitive tumor-specific markers. A comprehensive untargeted metabolomics study was conducted using exosome samples extracted from the serum of 48 subjects (36 HCC patients and 12 healthy controls) via a commercial kit. An ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) strategy was used to identify the metabolic compounds. A total of 18 differential metabolites were identified using the non-targeted metabolomics approach of UPLC-QTOF-MS/MS. …

Clinical And Genomic-Based Decision Support System To Define The Optimal Timing Of Allogeneic Hematopoietic Stem-Cell Transplantation In Patients With Myelodysplastic Syndromes, Cristina Astrid Tentori, Caterina Gregorio, Marie Robin, Nico Gagelmann, Carmelo Gurnari, Juan Carlos Caballero Berrocal, Saverio D'Amico, Marta Spreafico, Giulia Maggioni, Erica Travaglino, Elisabetta Sauta, Manja Meggendorfer, Lin-Pierre Zhao, Alessia Campagna, Victor Savevski, Armando Santoro, Najla Al Ali, David Sallman, Francesc Sole, Guillermo Garcia-Manero, Ulrich Germing, Nicolaus Kroger, Shahram Kordasti, Valeria Santini, Guillermo Sanz, Wolfgang Kern, Uwe Platzbecker, Maria Diez-Campelo, Jaroslaw P Maciejewski, Lionel Ades, Pierre Fenaux, Torsten Haferlach, Amer M Zeidan, Gastone Castellani, Rami Komrokji, Francesca Ieva, Matteo Giovanni Della Porta, Genomed4all And Synthema Consortiums

Faculty, Staff and Student Publications

Purpose: Allogeneic hematopoietic stem-cell transplantation (HSCT) is the only potentially curative treatment for patients with myelodysplastic syndromes (MDS). Several issues must be considered when evaluating the benefits and risks of HSCT for patients with MDS, with the timing of transplantation being a crucial question. Here, we aimed to develop and validate a decision support system to define the optimal timing of HSCT for patients with MDS on the basis of clinical and genomic information as provided by the Molecular International Prognostic Scoring System (IPSS-M).

Patients and methods: We studied a retrospective population of 7,118 patients, stratified into training and validation …

Multiple Guidance Mechanisms Control Axon Growth To Generate Precise T-Shaped Bifurcation During Dorsal Funiculus Development In The Spinal Cord, Bridget M. Curran, Kelsey R. Nickerson, Andrea R. Yung, Lisa V. Goodrich, Alexander Jaworski, Marc Tessier-Lavigne, Le Ma

Farber Institute for Neuroscience Faculty Papers

The dorsal funiculus in the spinal cord relays somatosensory information to the brain. It is made of T-shaped bifurcation of dorsal root ganglion (DRG) sensory axons. Our previous study has shown that Slit signaling is required for proper guidance during bifurcation, but loss of Slit does not affect all DRG axons. Here, we examined the role of the extracellular molecule Netrin-1 (Ntn1). Using wholemount staining with tissue clearing, we showed that mice lacking Ntn1 had axons escaping from the dorsal funiculus at the time of bifurcation. Genetic labeling confirmed that these misprojecting axons come from DRG neurons. Single axon analysis …

08.19.2024 Orsp Connect, Liz Williamson

ORED Newsletter

Lei Cao NSF award

FDP Meeting Summaries Available

August LINC Lunch

Collaboration Opportunities

Simulation Of Crispr-Cas9 Editing On Evolving Barcode And Accuracy Of Lineage Tracing

Faculty, Staff and Students Publications

We designed a simulation program that mimics the CRISPR-Cas9 editing on evolving barcode and double strand break repair procedure along with cell divisions. Emerging barcode mutations tend to build upon previously existing mutations, occurring sequentially with each generation. This process results in a unique mutation profile in each cell. We sample the barcodes in leaf cells and reconstruct the lineage, comparing it to the original lineage tree to test algorithm accuracy under different parameter settings. Our computational simulations validate the reasonable assumptions deduced from experimental observations, emphasizing that factors such as sampling size, barcode length, multiple barcodes, indel probabilities, and …

Interventional Radiology's Exploration Into Artificial Intelligence, Raymond Nguyen

Master's Projects and Capstones

Background: Artificial intelligence (AI) has become more prominent in our daily lives in recent years. This includes various aspects of healthcare. Interventional radiology (IR) is one of these specialties that has taken strides in understanding how AI can be leveraged for patient care. This literature review aims to understand what areas will be most impacted by AI in IR and how it will influence both the patient and interventional radiologist.

Methods: Twenty-six publications from 2019-2024 were selected from PubMed and Scopus. Publications were sourced through a combination of keywords, subject headings (MeSH terms), and citation searching.

Results: This literature review …

Human-Human Vs Human-Ai Therapy: An Empirical Study, Mohammad Amin Kuhail, Nazik Alturki, Justin Thomas, Amal K. Alkhalifa, Amal Alshardan

All Works

In many nations, demand for mental health services currently outstrips supply, especially in the area of talk-based psychological interventions. Within this context, chatbots (software applications designed to simulate conversations with human users) are increasingly explored as potential adjuncts to traditional mental healthcare service delivery with a view to improving accessibility and reducing waiting times. However, the effectiveness and acceptability of such chatbots remains under-researched. This study evaluates mental health professionals’ perceptions of Pi, a relational Artificial Intelligence (AI) chatbot, in the early stages of the psychotherapeutic process (problem exploration). We asked 63 therapists to assess therapy transcripts between a human …

Racial Identity Development And Imposter Phenomenon As Predictors Of Counselor Self-Efficacy, Erica D. Wade-Ball, Dana T. Isawi, Teresa A. Fisher

Journal of Counselor Preparation and Supervision

The authors utilized a correlational research design to examine the role of racial identity development and impostor phenomenon in predicting counselor self-efficacy among counselors-in-training of color. Racial identity development significantly predicts counselor self-efficacy, and imposter phenomenon is correlated with counselor self-efficacy. Based on the findings, the authors provide implications and recommendations for counselor educators and supervisors.

Development Of Vla4 And Cxcr4 Antagonists For The Mobilization Of Hematopoietic Stem And Progenitor Cells, Peter G Ruminski, Michael P Rettig, John F Dipersio

2020-Current year OA Pubs

The treatment of patients diagnosed with hematologic malignancies typically includes hematopoietic stem cell transplantation (HSCT) as part of a therapeutic standard of care. The primary graft source of hematopoietic stem and progenitor cells (HSPCs) for HSCT is mobilized from the bone marrow into the peripheral blood of allogeneic donors or patients. More recently, these mobilized HSPCs have also been the source for gene editing strategies to treat diseases such as sickle-cell anemia. For a HSCT to be successful, it requires the infusion of a sufficient number of HSPCs that are capable of adequate homing to the bone marrow niche and …

Hyperpolarized Magnetic Resonance Imaging, Nuclear Magnetic Resonance Metabolomics, And Artificial Intelligence To Interrogate The Metabolic Evolution Of Glioblastoma, Xiaoqian Jiang, Pratip K Bhattacharya, Shyan Shams

Faculty, Staff and Student Publications

Glioblastoma (GBM) is a malignant Grade VI cancer type with a median survival duration of only 8-16 months. Earlier detection of GBM could enable more effective treatment. Hyperpolarized magnetic resonance spectroscopy (HPMRS) could detect GBM earlier than conventional anatomical MRI in glioblastoma murine models. We further investigated whether artificial intelligence (A.I.) could detect GBM earlier than HPMRS. We developed a deep learning model that combines multiple modalities of cancer data to predict tumor progression, assess treatment effects, and to reconstruct in vivo metabolomic information from ex vivo data. Our model can detect GBM progression two weeks earlier than conventional MRIs …

Hybridizing Mechanistic Modeling And Deep Learning For Personalized Survival Prediction After Immune Checkpoint Inhibitor Immunotherapy, Joseph D Butner, Prashant Dogra, Caroline Chung, Eugene J Koay, James W Welsh, Vittorio Cristini

Faculty, Staff and Student Publications

We present a study where predictive mechanistic modeling is combined with deep learning methods to predict individual patient survival probabilities under immune checkpoint inhibitor (ICI) immunotherapy. This hybrid approach enables prediction based on both measures that are calculable from mechanistic models of key mechanisms underlying ICI therapy that may not be directly measurable in the clinic and easily measurable quantities or patient characteristics that are not always readily incorporated into predictive mechanistic models. A deep learning time-to-event predictive model trained on a hybrid mechanistic + clinical data set from 93 patients achieved higher per-patient predictive accuracy based on event-time concordance, …

In Reply: Can Artificial Intelligence Make The Cut? Dissecting Large Language Model’S Surgical Exam Performance, Adam M. Ostrovsky, Joshua R. Chen, Vishal N. Shah, Babak Abai

Department of Surgery Faculty Papers

No abstract provided.

Dominance Analysis To Assess Solute Contributions To Multicomponent Phase Equilibria, Daoyuan Qian, Hannes Ausserwoger, Tomas Sneideris, Mina Farag, Rohit V Pappu, Tuomas P J Knowles

2020-Current year OA Pubs

Phase separation in aqueous solutions of macromolecules underlies the generation of biomolecular condensates in cells. Condensates are membraneless bodies, representing dense, macromolecule-rich phases that coexist with the dilute, macromolecule-deficient phases. In cells, condensates comprise hundreds of different macromolecular and small molecule solutes. How do different solutes contribute to the driving forces for phase separation? To answer this question, we introduce a formalism we term energy dominance analysis. This approach rests on analysis of shapes of the dilute phase boundaries, slopes of tie lines, and changes to dilute phase concentrations in response to perturbations of concentrations of different solutes. The framework …

The Bioremediation Effect Of Microalgae On Wastewater: A Green Technology Approach, Mohamed Ahmed Reda Hamed Dr, Marwa Abdelfattah Abdallah Dr

Journal of Engineering Research

The present study lays an emphasis on the microalgae-based for simultaneous wastewater bioremediation using Chlorella vulgaris and Micrococcus luteus mixed algal cultures to remove its constituent pollutants, amazing green technology guarantees benefits with the decrease in the formation of dangerous solid sludge. Ten days of fully monitoring laboratory experimental program were performed in batch cultures to investigate the effect of various dominant mixing ratios for attaining wastewater concentrations and different governing temperature ranges on the performance of microalgae treatment. The results revealed that there is a significant impact of both wastewater concentrations and temperature treatment conditions on the capability of …

Indicators And Evidence Of Environmental Sustainability For Pedestrian In Public Parks (Towards An Approach For Formulating A Guideline Evaluation Model), Nashwa Youssif

Journal of Engineering Research

يتناول البحث أحد المجالات التي فرضت تواجدها في الأونة الأخيرة علي الساحة العلمية والبحثية التي تتعلق بالعلاقة التبادلية التأثير بين الإنسان والفراغ العمراني حيث يتنامي الإهتمام بالخصائص الإنسانيه و مدي توافقها مع هذا الفراغ العمراني.

وتعد مسارات المشاة من أهم الحيزات العمرانية التى تشكل النسيج العمراني وأحد أهم وسائل التواصل الإجتماعي والثقافي والوظيفي نظرآ لإرتباطها بالغالبية العظمي من أفراد المجتمع، ومساعدتها على جذب العديـد من الأنشطة داخل الحدائق العامة. مما يشير إلي ضرورة الإهتمام بتحسين بيئة حركة المشاه كمدخل للتواصل والإستدامة.

ومن هنا تتمثل مشكلة البحث في نقص الدراسات حول تقييم العلاقة بين معايير الاستدامة التصميمية والنظم البيئية لمسارات المشاة …

Cluster Effect For Snp-Snp Interaction Pairs For Predicting Complex Traits, Hui Yi Lin, Harun Mazumder, Indrani Sarkar, Po Yu Huang, Rosalind A. Eeles, Zsofia Kote-Jarai, Kenneth R. Muir, Johanna Schleutker, Nora Pashayan, Jyotsna Batra, David E. Neal, Sune F. Nielsen, Børge G. Nordestgaard, Henrik Grönberg, Fredrik Wiklund, Robert J. Macinnis, Christopher A. Haiman, Ruth C. Travis, Janet L. Stanford, Adam S. Kibel, Cezary Cybulski, Kay Tee Khaw, Christiane Maier, Stephen N. Thibodeau, Manuel R. Teixeira, Lisa Cannon-Albright, Hermann Brenner, Radka Kaneva, Hardev Pandha, Et Al

School of Public Health Faculty Publications

Single nucleotide polymorphism (SNP) interactions are the key to improving polygenic risk scores. Previous studies reported several significant SNP-SNP interaction pairs that shared a common SNP to form a cluster, but some identified pairs might be false positives. This study aims to identify factors associated with the cluster effect of false positivity and develop strategies to enhance the accuracy of SNP-SNP interactions. The results showed the cluster effect is a major cause of false-positive findings of SNP-SNP interactions. This cluster effect is due to high correlations between a causal pair and null pairs in a cluster. The clusters with a …

Cycle Syncing: Optimizing Women's Quality Of Life, Megan Francois

Theses and Graduate Projects

A woman’s hormones are in constant fluctuation throughout the menstrual cycle. This 28-day, on average, fluctuation can cause major shifts in mood, cognition, exercise tolerance, and nutrition needs. Because of this, there is potential to optimize quality of life if each phase is synced with diet, exercise, and complementary medicine utilizing holistic methods. Implications for further research include a need for additional longitudinal and prospective studies. Factors that need to be addressed include further analysis of the windows of vulnerability over the menstrual cycle according to female hormone fluctuations, effects of hormonal contraceptives, and effects of pathology on the cycle.

Digital Scribes: A Possible Solution For Provider Burnout By Reducing Provider Workload, Shannon Storley

Theses and Graduate Projects

Background: Provider burnout is continuing to be a massive problem for our healthcare industry. One major contributor to provider burnout is burdensome administrative tasks associated with documentation of electronic medical records (EMR). This review aims to uncover the applications for artificially intelligent digital scribes as a solution to reduce EMR documentation burden. Purpose: Provider burnout has shown to increase the incidence of major mistakes and decreased patient safety grades. Digital scribes could be a solution in reducing provider burnout by reducing the administrative burden of EMR documentation. Methods: A comprehensive literature review was conducted using articles from PubMed using search …

Aquatics As A Therapeutic Intervention And Its Effects On The Quality Of Life Of People Diagnosed With Amyotrophic Lateral Sclerosis, Brianna Barcelo, Lakesia Boykin, Helen Carey

Summer 2024 OTD Capstone Symposium

: Interventions in the form of aquatics have been utilized with the profession of occupational therapy as the aquatic environment is a model setting for addressing occupational therapy interests (Becker, 2009). Although aquatic interventions are utilized within profession, there is limited research discussing how aquatics as a therapeutic intervention effects the quality of life (QoL) of people diagnosed with ALS. Therefore, the purpose of the research project was to explore the effects of aquatics as a therapeutic intervention on the QoL of those diagnosed with ALS.