Analytical, Diagnostic and Therapeutic Techniques and Equipment Commons^™

Irnet: Immunotherapy Response Prediction Using Pathway Knowledge-Informed Graph Neural Network, Yuexu Jiang, Manish Sridhar Immadia, Duolin Wang, Shuai Zeng, Yen On Chan, Jing Zhou, Dong Xu, Trupti Joshi

Biomedical Sciences

Introduction: Immune checkpoint inhibitors (ICIs) are potent and precise therapies for various cancer types, significantly improving survival rates in patients who respond positively to them. However, only a minority of patients benefit from ICI treatments.

Objectives: Identifying ICI responders before treatment could greatly conserve medical resources, minimize potential drug side effects, and expedite the search for alternative therapies. Our goal is to introduce a novel deep-learning method to predict ICI treatment responses in cancer patients.

Methods: The proposed deep-learning framework leverages graph neural network and biological pathway knowledge. We trained and tested our method using ICI-treated patients’ data from several …

Whole-Exome Sequencing Identified Molecular Variants Linked To The Progression Of Gastric Precancerous Lesions In Patients From Southwestern Colombia—An Exploratory Approach., Lizeth Mejia-Ortiz, Jovanny Zabaleta, Jone Garai, Luis Eduardo Bravo, Andres Castillo

School of Graduate Studies Faculty Publications

No abstract provided.

Surveying Management Strategies For Pediatric Autoimmune Hepatitis, Lillie Baca

University Honors Theses

Pediatric autoimmune hepatitis (PAIH) is a long-term condition that requires ongoing treatment and regular monitoring. It is characterized by its elevation of liver enzymes, interface hepatitis, and the specific presence of circulating autoantibodies. There is a general lack of consensus on appropriate measures of diagnostic criteria, treatment medication, and beneficial practices for monitoring the disease. The existing literature contains several subtle discrepancies that challenge a practitioner's judgement for care management of children with autoimmune hepatitis. This study is a retrospective chart review aimed at understanding the current diagnostics, treatment, and long-term management strategies of PAIH at a single center. Also, …

Quantitative Analysis Using Mri Of Patients That Are High Risk For Pancreatic Cancer, Aqsa Tarik

University Honors Theses

Pancreatic ductal adenocarcinoma (PDAC) is a cancer that is detected in its later stages, causing its five-year survival rate of 2-9% (3). The majority of patients who develop PDAC unfortunately deal with a low survival rate due to the progression of the tumor in the body. Magnetic resonance imaging (MRI) can assess the structure of the tissue within organs in the body. These scans can also be used in order to detect and diagnose tumors, allowing them to be a generator of cancer biomarkers. PDAC isn’t distinguishable on conventional images, as the pancreas will appear normal, allowing the tumor progress …

A Scoping Review On The Integration Of Artificial Intelligence In Point-Of-Care Ultrasound: Current Clinical Applications, Junu Kim, Sandhya Maranna, Caterina Watson, Nayana Parange

Research outputs 2022 to 2026

Background: Artificial intelligence (AI) is used increasingly in point-of-care ultrasound (POCUS). However, the true role, utility, advantages, and limitations of AI tools in POCUS have been poorly understood. Aim: to conduct a scoping review on the current literature of AI in POCUS to identify (1) how AI is being applied in POCUS, and (2) how AI in POCUS could be utilized in clinical settings. Methods: The review followed the JBI scoping review methodology. A search strategy was conducted in Medline, Embase, Emcare, Scopus, Web of Science, Google Scholar, and AI POCUS manufacturer websites. Selection criteria, evidence screening, and selection were …

Pre-Amplification Of Cell-Free Dna: Balancing Amplification Errors With Enhanced Sensitivity, Wei Yen Chan, Ashleigh Stewart, Russell J. Diefenbach, Elin S. Gray, Jenny H. Lee, Richard A. Scolyer, Georgina V. Long, Helen Rizos

Research outputs 2022 to 2026

Circulating tumour DNA (ctDNA) is a promising biomarker for personalised oncology. However, its clinical utility is limited by detection sensitivity, particularly in early-stage disease. T-Oligo Primed Polymerase Chain Reaction (TOP-PCR) is a commercial amplification approach utilising an efficient “half-adapter” ligation design and a single-primer-based PCR strategy. This study evaluated the clinical value and application of cell-free DNA (cfDNA) pre-amplification. cfDNA amplification with TOP-PCR preserved DNA size profiles and resulted in a 22 bp size increase due to the half-adaptor ligation. Gene target amplification rates varied, showing lower efficiency for the GC-rich TERT promoter amplicon and higher efficiency for the BRAF …

Of Dolls And Jewels : Keeping As A Strategy Of Care And Belonging, Yuqi Fan

Masters Theses

In this thesis, I will discuss the psychology behind object attachment in the doll-keeping subculture by integrating doll language into contemporary jewelry. I researched the Chinese term “Pi” as an accurate way of explaining how doll-keepers are attached to their dolls. In this 21st century, the widespread use of social media and AI technologies have deepened people's reliance on virtual spaces, leading to emotional detachment in our society. Adopting the concept of “Pi” into contemporary jewelry, which encourages a shift in focus towards external objects, the practice of doll-keeping becomes a form of self-care that compensates for our current loneliness …

Barriers To Clinical Cosmetic And Laser Dermatology Research In The Academic Setting By Source Of Funding: A Systematic Review, Bianca Y. Kang, Saranya P. Wyles, Yakir Levin, Rawaa Almukhtar, Stephanie R. Jackson Cullison, Jayne S. Joo, Sami K. Saikaly, Shalinie Mahadeo, Michael Ong, Sophia Salingaros, Maria Hordinsky, Sarah A. Ibrahim, Devina Mehta, Shoko Mori, Edit B. Olasz Harken, Diana Bolotin, Kira Minkis, Murad Alam

Department of Dermatology and Cutaneous Biology Faculty Papers

Clinical research is a cornerstone of academic dermatology, including research in cosmetic and laser procedures. However, numerous barriers exist to conducting clinical research in an academic setting as compared to private practice. The objective of this study was to describe the barriers to clinical research in cosmetic and laser dermatology in the academic setting under three common funding scenarios: (1) industry sponsored, (2) unfunded, investigator-initiated, and (3) publicly funded, investigator-initiated. A systematic review of the literature was conducted to identify 17 publications regarding funding of clinical dermatology research. Inductive content analysis was used to extract, categorize, and understand the barriers …

Colorectal Cancer And The Risk Of Mortality Among Individuals With Suicidal Ideation, Srikanta Banerjee, Jagdish Khubchandani, Stanley Nkemjika

Department of Psychiatry and Human Behavior Faculty Papers

Suicide is a major public health problem that has grown at alarming rates in the last two decades. Colorectal cancer (CRC) is one of the most common causes of cancer deaths in the United States in both males and females. However, the influence of suicidal ideation (SI) on the association between CRC and risk of mortality has not been well examined.

METHODS: For this study, the 2005-2018 National Health and Nutrition Examination Survey (NHANES), a nationally representative survey of United States adults aged 20 years or older, was utilized. CRC survivorship was determined from self-reported data on CRC, and mortality …

Neovascular Pruning By Ido1 Inhibitors Can Potentiate Immunogenic Cytotoxicity Of Ischemia-Targeted Agents To Synergistically Enhance Anti-Pd-1 Responsiveness, Shih-Chun Shen, Souvik Dey, James B. Duhadaway, Erika Sutanto-Ward, Maurice T. Hampton, Serguei V. Kozlov, George C. Prendergast, Alexander J. Muller

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

BACKGROUND: Strategies for deploying indoleamine 2,3-dioxygenase 1 (IDO1)-targeted therapies for use against cancer have focused on IDO1's role in promoting peripheral immune tolerance that shields tumors from effector T cells. However, preclinical investigation of both primary and metastatic tumor development in the lungs has uncovered a previously unappreciated role for IDO1 in directing a counterregulatory response to interferon (IFN)-γ that realigns the local inflammatory environment to promote tumor neovascularization. Understanding how to therapeutically leverage the ability of IDO1 inhibitors to subvert inflammatory neovascularization within the tumor microenvironment has potential ramifications for future clinical development of these compounds.

METHODS: Pulmonary metastases …

Integrating Radiogenomics And Machine Learning In Musculoskeletal Oncology Care, Rahul Kumar, Kyle Sporn, Akshay Khanna, Phani Paladugu, Chirag Gowda, Alex Ngo, Ram Jagadeesan, Nasif Zaman, Alireza Tavakkoli

Department of Medicine Faculty Papers

Musculoskeletal tumors present a diagnostic challenge due to their rarity, histological diversity, and overlapping imaging features. Accurate characterization is essential for effective treatment planning and prognosis, yet current diagnostic workflows rely heavily on invasive biopsy and subjective radiologic interpretation. This review explores the evolving role of radiogenomics and machine learning in improving diagnostic accuracy for bone and soft tissue tumors. We examine integrating quantitative imaging features from MRI, CT, and PET with genomic and transcriptomic data to enable non-invasive tumor profiling. AI-powered platforms employing convolutional neural networks (CNNs) and radiomic texture analysis show promising results in tumor grading, subtype differentiation …

Decompression With Intradural Dissection For The Chiari Malformation Type I: Toward Eliminating Wound Complications, Anna Lin, Lindsey Asti, Marissa Carroll, Jeffrey Campbell, Jospeh Piatt

Department of Neuroscience Faculty Papers

BACKGROUND: There is continuing conversation about surgical technique in the management of the Chiari malformation. Popular options include osseous decompression alone, decompression with dural splitting, and decompression with intradural dissection (DID) and duraplasty. Wound complications after intradural dissection are a persistent problem. The current study of an institutional series examines wound complication rates after intradural dissection without dural closure.

METHODS: A retrospective single-institution chart review was performed for patients < 21 years with Chari malformation type I who underwent DID without dural closure and had at least 6 months of follow-up. Bone removal corresponded to the area of attachment of the rectus capitis posterior minor muscles together with laminectomy of the atlas. The trapezius and semispinalis capitis muscles were retracted but were not separated from the occiput.

RESULTS: A total of 76 patients were treated from May 2010 through May 2024. Thirty-eight (50.0%) patients had syringomyelia. The median age at surgery was 9 years (interquartile range [IQR] 4-13), …

Consideration Of Anesthesia Techniques For Deep Brain Stimulation Implantation In The Treatment Of Drug-Resistant Epilepsy: A Narrative Review, Alan D. Kaye, Benjamin Esneault, Shreya Deshpande, Joseph Wentling, Shahab Ahmadzadeh, Pooja Potharaju, Sahar Shekoohi

School of Medicine Faculty Publications

Epilepsy is a neurological disorder characterized by recurrent, unprovoked seizures, affecting millions worldwide. While anti-seizure medications serve as first-line treatment, approximately one-third of patients develop drug-resistant epilepsy (DRE), necessitating alternative interventions. Deep brain stimulation (DBS) has emerged as a promising therapy for DRE, particularly for patients who are ineligible for resective surgery. DBS involves stereotactic implantation of electrodes into target brain regions, such as the anterior nucleus of the thalamus (ANT), centromedian nucleus (CMT), and hippocampus (HC), to modulate aberrant neural activity and to reduce seizure frequency. Anesthesia plays a critical role in DBS implantation, influencing both patient safety and …

Cardiac Amyloid, The Great Imitator, Nolan R. Fox, Nicholas J. Fox, Emily Newman, Brian Osler, Eugene Storozynsky

Division of Cardiology Faculty Papers

BACKGROUND: Although endomyocardial biopsy (EMB) is the criterion standard for diagnosis of infiltrative cardiac disease, cardiac sarcoidosis (CS) or cardiac amyloid can be diagnosed noninvasively through both clinical suspicion and advanced imaging techniques of cardiac magnetic resonance imaging (CMR) or cardiac positron emission tomography (PET).

CASE SUMMARY: A 79-year-old man with mediastinal sarcoidosis presented with new chest pain and a right bundle branch block, raising concern for CS. CMR and cardiac PET also supported the diagnosis of CS, but EMB ultimately revealed transthyretin amyloid cardiomyopathy. The patient was started on tafamidis and showed improvement at 1-year follow-up.

DISCUSSION: This case …

Histodx: Revolutionizing Breast Cancer Diagnosis Through Advanced Imaging Techniques, Wishal Arshad, Tehreem Masood, H. M. Shahzad, Hassan A. Ahmed, Syed Hamza Ahmed, Hafiz Muhammad Tayyab Khushi

Business Faculty Publications

Breast cancer is the second leading cause of mortality among women worldwide, highlighting the need for efficient histopathology-based screening methods for early diagnosis. This study introduces HistoDX, a deep learning framework to classify Invasive Ductal Carcinoma (IDC) using 277,524 histopathology image patches (50x50 pixels) from Paul Mooney’s IDC dataset on Kaggle, comprising No Cancer and IDC(+) classes. HistoDX employs a preprocessing pipeline with normalization, data augmentation, and class balancing via oversampling and weighted loss to address the class imbalance. A customized convolutional neural network, built on EfficientNetV2-B3 with additional layers, achieves 97% accuracy and a 0.91 ROC-AUC score on the …

A Smart Pill Bottle And Text Messaging Intervention For Promoting Medication Adherence In Patients With Chronic Myeloid Leukemia: A Pilot Study Of Txt4 Tki, Kuang-Yi Wen, Neil Palmisiano, Rita Smith, Rachel Slamon, Gina Keiffer, Christian Fidler, Margaret Kasner, Lindsay Wilde, Md

Department of Medical Oncology Faculty Papers

BACKGROUND: Patients undergoing tyrosine kinase inhibitor (TKI) therapy for chronic myeloid leukemia (CML) often face challenges with adherence, despite the efficacy of the treatment. Theory-guided and evidence-informed interventions addressing psychosocial and adherence barriers are critical for promoting adherence. Using a mixed-method approach, the pilot study developed and evaluated the feasibility and potential impact of an intervention "txt4TKI," to support medication and symptom management among CML patients undergoing TKI therapy.

METHODS: Guided by the Necessity and Concerns framework, the study comprised two phases: Phase 1 involved qualitative patient needs assessment interviews informing intervention design. Phase 2 was a single-arm pilot study …

Imaging Hallmarks Of Idiopathic Intracranial Hypertension And Insights Into Pathogenesis, Albalooshy Basimah, Scott Faro, Hsiangkuo Yuan, Kiran Talekar, Prabath Mondel, Enchao Qiu, Joga Chaganti

Department of Radiology Faculty Papers

Idiopathic Intracranial hypertension (IIH), also referred to as pseudotumor cerebri, is a term used to describe increased intracranial pressure in the absence of a known identifiable secondary cause. Despite advancements of neuroimaging techniques, imaging of the pathological underpinnings in the diagnosis of IIH has been limited. Although the causation of IIH has been ascribed to increased Cerebrospinal Fluid production and disordered drainage through the dural sinuses, new evidence shows that the glymphatic system which is an alternate pathway of drainage is likely to play a pivotal role. In this review, we address the pathophysiological underpinnings in the causation of IIH …

Viral Detection In Anterior Nasal Swabs Versus Nasopharyngeal Swabs In Children, Nicole Neeley, Abby Kietzman, Rangaraj Selvarangan, Dithi Banerjee, Jennifer Goldman, Jennifer Schuster

Research Days

Background: Respiratory viruses are a significant cause of pediatric illness and healthcare utilization. Diagnostic testing for respiratory viruses is generally performed using nasopharyngeal (NP) specimens obtained by trained staff, limiting testing to medical settings. Evaluating additional sampling methods in children that are easier to collect and can be performed outside of medical settings, such as anterior nasal swab (NS) specimens may expand access to diagnostic testing and aid public health surveillance.

Methods: Eligible children hospitalized at Children’s Mercy Hospital who had a standard of care NP specimen collected for respiratory viral testing were enrolled. Research NS specimens were obtained through …

Tacrolimus Dosing In Liver Transplant Recipients Using Phenotypic Personalized Medicine: A Phase 2 Randomized Clinical Trial, Jeffrey Khong, Megan Lee, Curtis Warren, Un Kim, Sergio Duarte, Kenneth Andreoni, Sunaina Shrestha, Mark Johnson, Narendra Battula, Danielle Mckimmy, Thiago Beduschi, Ji-Hyun Lee, Derek Li, Chih-Ming Ho, Ali Zarrinpar

Department of Surgery Faculty Papers

Tacrolimus is the most commonly used immunosuppression drug after solid organ transplantation; however, its dosing is challenging due to substantial inter-individual variability, often resulting in blood levels that deviate from the target therapeutic range. We explored whether a dynamically customized, phenotypic-outcome-guided drug dosing method could improve maintenance of drug trough levels within pre-determined target ranges, focusing on tacrolimus immediately after liver transplantation. This single-center, partially blinded, completed clinical trial involved 62 adults undergoing liver transplantation, block randomized into parallel groups: standard-of-care (SOC) clinician-determined or Phenotypic Personalized Medicine (PPM)-guided tacrolimus dosing. The primary outcome was percentage of post-transplant days with large …

Effect Of Endodontic Access Preparation On The Retention Of Zirconia Crowns With Temporary Or Permanent Access Hole Restorations: An In Vitro Study, J. Nick Sanders, Amir H. Nejat, Peter Dupree, Edwin Kee, Madeleine E. Raymond, Fred Mcmullen

School of Dentistry Faculty Publications

Objectives: To evaluate the effect endodontic access preparation had on the retention of anterior zirconia crowns after restoring the access hole with temporary versus permanent restorative materials. Methods: 30 anterior zirconia crowns were milled from 5Y-TZP zirconia and bonded to a 3D printed die with resin cement. Crowns were randomly divided into three groups including negative control (NC, n = 10) with no endodontic access preparation; positive control (PC, N = 10) received endodontic access preparation and was restored with a temporary restorative material (Cavit); composite restoration (CR, N = 10) received an endodontic access preparation and then the access …