Medical Specialties Commons^™

An Essential Gene Signature Of Breast Cancer Metastasis Reveals Targetable Pathways, Yiqun Zhang, Fengju Chen, Marija Balic, Chad J Creighton

Faculty, Staff and Students Publications

BACKGROUND: The differential gene expression profile of metastatic versus primary breast tumors represents an avenue for discovering new or underappreciated pathways underscoring processes of metastasis. However, as tumor biopsy samples are a mixture of cancer and non-cancer cells, most differentially expressed genes in metastases would represent confounders involving sample biopsy site rather than cancer cell biology.

METHODS: By paired analysis, we defined a top set of differentially expressed genes in breast cancer metastasis versus primary tumors using an RNA-sequencing dataset of 152 patients from The Breast International Group Aiming to Understand the Molecular Aberrations dataset (BIG-AURORA). To filter the genes …

A Rare Case Of Disseminated Extra-Nodal Natural Killer (Nk) Cell Lymphoma, Sowbharnika Arivazhagan, Guru Prasad Parthiban, Sukanthini Subbiah

School of Medicine Faculty Publications

Extranodal Natural Killer (NK)/T-cell lymphoma, nasal type, is rare and frequently found in Asia and South America. It is rarely found in the United States, mainly in the immigrant population. We present a 26-year-old male from Central America who was found to have disseminated NK/T-cell lymphoma. Through this article, we explain how we manage our patient and try to consolidate the treatment modalities for different stages of the disease.

Slow Proliferation Of Bap1-Deficient Uveal Melanoma Cells Is Associated With Reduced S6 Signaling And Resistance To Nutrient Stress, Vivian Chua, Melisa Lopez-Anton, Mizue Terai, Ryota Tanaka, Usman Baqai, Timothy J Purwin, Jelan I Haj, Francis J Waltrich, Isabella Trachtenberg, Kristine Luo, Rohith Tudi, Angela Jeon, Anna Han, Inna Chervoneva, Michael A Davies, Julio A Aguirre-Ghiso, Takami Sato, Andrew E Aplin

Faculty, Staff and Student Publications

Uveal melanoma (UM) is the deadliest form of eye cancer in adults. Inactivating mutations and/or loss of expression of the gene encoding BRCA1-associated protein 1 (BAP1) in UM tumors are associated with an increased risk of metastasis. To investigate the mechanisms underlying this risk, we explored the functional consequences of BAP1 deficiency. UM cell lines expressing mutant BAP1 grew more slowly than those expressing wild-type BAP1 in culture and in vivo. The ability of BAP1 reconstitution to restore cell proliferation in BAP1-deficient cells required its deubiquitylase activity. Proteomic analysis showed that BAP1-deficient cells had decreased phosphorylation of ribosomal S6 and …

Role Of Ethanolamine Utilization And Bacterial Microcompartment Formation In Listeria Monocytogenes Intracellular Infection, Ayan Chatterjee, Karan Gautam Kaval, Danielle A Garsin

Faculty, Staff and Student Publications

Ethanolamine (EA) affects the colonization and pathogenicity of certain human bacterial pathogens in the gastrointestinal tract. However, EA can also affect the intracellular survival and replication of host cell invasive bacteria such as Listeria monocytogenes (LMO) and Salmonella enterica serovar Typhimurium (S. Typhimurium). The EA utilization (eut) genes can be categorized as regulatory, enzymatic, or structural, and previous work in LMO showed that loss of genes encoding functions for the enzymatic breakdown of EA inhibited LMO intracellular replication. In this work, we sought to further characterize the role of EA utilization during LMO infection of host …

Navigating Diagnostic And Treatment Challenges Of Pulmonary Hypertension In Infants With Bronchopulmonary Dysplasia., Nidhy P. Varghese, Gabriel Altit, Megan M. Gubichuk, Roopa Siddaiah

Manuscripts, Articles, Book Chapters and Other Papers

Advances in perinatal intensive care have significantly enhanced the survival rates of extremely low gestation-al-age neonates but with continued high rates of bronchopulmonary dysplasia (BPD). Nevertheless, as the survival of these infants improves, there is a growing awareness of associated abnormalities in pulmonary vascular development and hemodynamics within the pulmonary circulation. Premature infants, now born as early as 22 weeks, face heightened risks of adverse development in both pulmonary arterial and venous systems. This risk is compounded by parenchymal and airway abnormalities, as well as factors such as inflammation, fibrosis, and adverse growth trajectory. The presence of pulmonary hypertension in …

Hemojuvelin-Mediated Hepcidin Induction Requires Both Bone Morphogenetic Protein Type I Receptors Alk2 And Alk3, Deniz Y Dogan, Eugen I Urzica, Isabelle Hornung, Philipp Kastl, David Oguama, Franca M Fette, Lien H Nguyen, Frank Rosenbauer, Kai Zacharowski, Ursula Klingmüller, Elise Gradhand, Andreas Von Knethen, Rüdiger Popp, Ingrid Fleming, Lisa Schrader, Andrea U Steinbicker

Faculty, Staff and Student Publications

Hemojuvelin (HJV) is a glycosylphosphatidylinositol-anchored protein of the repulsive guidance molecule family acting as a bone morphogenetic protein (BMP) coreceptor to induce the hepatic iron regulatory protein hepcidin. Hepcidin causes ubiquitination and degradation of the sole known iron exporter ferroportin, thereby limiting iron availability. The detailed signaling mechanism of HJV in vivo has yet to be investigated. In the current manuscript, we used an established model of adeno-associated virus (AAV)-mediated liver-specific overexpression of HJV in murine models of hepatocyte-specific deficiency of the BMP type I receptors Alk2 or Alk3. In control mice, HJV overexpression increased hepatic Hamp messenger RNA (mRNA) …

Therapy-Related Chronic Myelomonocytic Leukemia Does Not Have The High-Risk Features Of A Therapy-Related Neoplasm, Alex Bataller, Georgina Gener-Ricos, Emmanuel Almanza-Huante, Kelly S Chien, Samuel Urrutia, Alexandre Bazinet, Juan Jose Rodriguez-Sevilla, Danielle Hammond, Koji Sasaki, Koichi Takahashi, Courtney D Dinardo, Farhad Ravandi, Gautam Borthakur, Tapan M Kadia, Rashmi Kanagal-Shamanna, Hagop M Kantarjian, Guillermo Garcia-Manero, Guillermo Montalban-Bravo

Faculty, Staff and Student Publications

Therapy-related myeloid neoplasms (t-MNs) arise after exposure to cytotoxic therapies and are associated with high-risk genetic features and poor outcomes. We analyzed a cohort of patients with therapy-related chronic myelomonocytic leukemia (tCMML; n = 71) and compared its features to that of de novo CMML (dnCMML; n = 461). Median time from cytotoxic therapy to tCMML diagnosis was 6.5 years. Compared with dnCMML, chromosome-7 abnormalities (4% vs 13%; P = .005) but not complex karyotype (3% vs 7%; P = .15), were more frequent in tCMML. tCMML was characterized by higher TP53 mutation frequency (4% vs 12%; P = .04) …

Painful Shoulder Syndrome And Upper Limb Function In Competitive Swimmers, Beata Pożarowszczyk-Kuczko, Martyna Kumorek, Dariusz Mroczek, Filipe Clemente, Wioletta Dziubek

Baltic Journal of Health and Physical Activity

Introduction. Swimming is an athletic discipline that largely involves the upper limbs. Due to the driving and propulsive function, there is a heavy involvement of almost all muscles of the arm. Painful shoulder syndrome (PSS) is considered to be one of the main causes of interference with an effective and correct movement of the underwater stroke, which is a fundamental element of functionality in this discipline. The aim of this study was to evaluate whether PSS affects upper limb function in competitive swimmers. Material and methods. Thirty-two swimmers aged 17–24 years with at least 2nd sport class participated in the …

Collaborative Modeling To Compare Different Breast Cancer Screening Strategies: A Decision Analysis For The Us Preventive Services Task Force, Amy Trentham-Dietz, Christina Hunter Chapman, Jinani Jayasekera, Kathryn P Lowry, Brandy M Heckman-Stoddard, John M Hampton, Jennifer L Caswell-Jin, Ronald E Gangnon, Ying Lu, Hui Huang, Sarah Stein, Liyang Sun, Eugenio J Gil Quessep, Yuanliang Yang, Yifan Lu, Juhee Song, Diego F Muñoz, Yisheng Li, Allison W Kurian, Karla Kerlikowske, Ellen S O'Meara, Brian L Sprague, Anna N A Tosteson, Eric J Feuer, Donald Berry, Sylvia K Plevritis, Xuelin Huang, Harry J De Koning, Nicolien T Van Ravesteyn, Sandra J Lee, Oguzhan Alagoz, Clyde B Schechter, Natasha K Stout, Diana L Miglioretti, Jeanne S Mandelblatt

Faculty, Staff and Student Publications

IMPORTANCE: The effects of breast cancer incidence changes and advances in screening and treatment on outcomes of different screening strategies are not well known.

OBJECTIVE: To estimate outcomes of various mammography screening strategies.

DESIGN, SETTING, AND POPULATION: Comparison of outcomes using 6 Cancer Intervention and Surveillance Modeling Network (CISNET) models and national data on breast cancer incidence, mammography performance, treatment effects, and other-cause mortality in US women without previous cancer diagnoses.

EXPOSURES: Thirty-six screening strategies with varying start ages (40, 45, 50 years) and stop ages (74, 79 years) with digital mammography or digital breast tomosynthesis (DBT) annually, biennially, or …

Rigor And Reproducibility In Human Brain Organoid Research: Where We Are And Where We Need To Go, Soraya O Sandoval, Gerarda Cappuccio, Karina Kruth, Sivan Osenberg, Saleh M Khalil, Natasha M Méndez-Albelo, Krishnan Padmanabhan, Daifeng Wang, Mark J Niciu, Anita Bhattacharyya, Jason L Stein, André M M Sousa, Elisa A Waxman, Elizabeth D Buttermore, Dosh Whye, Carissa L Sirois, Cross-Iddrc Human Stem Cell Consortium, Aislinn Williams, Mirjana Maletic-Savatic, Xinyu Zhao

Faculty, Staff and Students Publications

Human brain organoid models have emerged as a promising tool for studying human brain development and function. These models preserve human genetics and recapitulate some aspects of human brain development, while facilitating manipulation in an in vitro setting. Despite their potential to transform biology and medicine, concerns persist about their fidelity. To fully harness their potential, it is imperative to establish reliable analytic methods, ensuring rigor and reproducibility. Here, we review current analytical platforms used to characterize human forebrain cortical organoids, highlight challenges, and propose recommendations for future studies to achieve greater precision and uniformity across laboratories.

Neuroimaging Evaluation Of The Long Term Impact Of A Novel Paired Meditation Practice On Brain Function, Andrew B. Newberg, Nancy Wintering, Chloe Hriso, Faezeh Vedaei, Sara Gottfried, Reneita Ross

Marcus Institute of Integrative Health Faculty Papers

BACKGROUND: A growing number of advanced neuroimaging studies have compared brain structure and function in long term meditators to non-meditators. The goal is to determine if there may be long term effects on the brain from practicing meditation. In this paper, we present new data on the long term effects of a novel meditation practice in which the focus is on clitoral stimulation. The findings from such a study have implications for potential therapeutic uses with regard to various neurological or psychiatric conditions.

METHODS: We evaluated the cerebral glucose metabolism in 40 subjects with an extended history (>1 year …

The Joint Effects Of Sleep And Pain, And Moderations By Work Characteristics, Christina Xuong Mu

USF Tampa Graduate Theses and Dissertations

Reactivity describes interindividual differences in the physiological or emotional responses following an antecedent stressor. For instance, higher stressor reactivity to shorter sleep (i.e., those who report greater stressor severity following shorter-than-usual sleep) and higher negative affective reactivity to stressors (i.e., those who report more negative affect following a stressful event) have worse mental and physical health. Pain reactivity to shorter sleep is a novel concept that describes differences in pain responses following a night of shorter-than-usual sleep. Higher pain reactivity to shorter sleep means that individuals report more pain locations or higher pain severity following shorter-than-usual sleep the previous night, …

Concepts In Animal Parasitology, Scott L. Gardner, Sue Ann Gardner

Zea E-Books Collection

Note that this version of the textbook has been superceded by the one updated in 2026, available at the UNL Pressbooks site.

The hard copy version that is for sale at lulu.com is the old version.

"This is a textbook covering concepts in animal parasitology. It is meant to be used by students, teachers, professors, researchers, and members of the public who are interested in learning about animal parasite biology, systematics, taxonomy, zoogeography, and ecology. The primary intended audience is upper-level undergraduate or graduate university students who have knowledge of basic biology and, particularly, basic animal biology. (863 pages, …

Author Correction: Long Noncoding Rna Malat1 Protects Against Osteoporosis And Bone Metastasis, Yang Zhao, Jingyuan Ning, Hongqi Teng, Yalan Deng, Marisela Sheldon, Lei Shi, Consuelo Martinez, Jie Zhang, Annie Tian, Yutong Sun, Shinichi Nakagawa, Fan Yao, Hai Wang, Li Ma

Faculty, Staff and Student Publications

This corrects the article "Long noncoding RNA Malat1 protects against osteoporosis and bone metastasis", 2384.

Morbidity And Mortality Following Hiatal Hernia Repair In Geriatric Patients: A Multicenter Research Network Study, Sunjay S. Kumar, Martina Rama, Scott Koeneman, Sami Tannouri, Talar Tatarian, Francesco Palazzo

Department of Surgery Faculty Papers

BACKGROUND: Hiatal hernia is a common surgical pathology. Such hernias can be found incidentally and patients may opt for an initial nonoperative approach though many will pursue surgery after symptom progression. Data on the effects of age on the outcomes of hiatal hernia repair may help inform this decision-making process.

METHODS: The TriNetX database was queried for all adult patients undergoing hiatal hernia repair from 2000 to 2023. Patients were divided into elective and emergent cohorts on the basis of diagnosis codes indicating obstruction or gangrene. Patients aged 80-89 were compared against those aged 65-79 in unadjusted analysis. Logistic regression …

Author Correction: The Frequency Of Pathogenic Variation In The All Of Us Cohort Reveals Ancestry-Driven Disparities, Eric Venner, Karynne Patterson, Divya Kalra, Marsha M Wheeler, Yi-Ju Chen, Sara E Kalla, Bo Yuan, Jason H Karnes, Kimberly Walker, Joshua D Smith, Sean Mcgee, Aparna Radhakrishnan, Andrew Haddad, Philip E Empey, Qiaoyan Wang, Lee Lichtenstein, Diana Toledo, Gail Jarvik, Anjene Musick, Richard A Gibbs, All Of Us Research Program Investigators

Faculty, Staff and Students Publications

Correction to: Communications Biology 10.1038/s42003-023-05708-y, published online 19 February 2024

The data availability statement was incorrectly given as “All sequencing data used in this study are available on the All of Us Researcher Workbench in the v7 release.” but should have been “All sequencing data used in this study are available on the All of Us Researcher Workbench in the v6 release”. The original Article has been corrected.

Echocardiogram By Apical-Subcostal Protocol In Prone Position During Invasive Mechanical Ventilation In Cardiovascular Intensive Care Unit, César Del Castillo, Fernando Verdugo, Franco Appiani, Francisca Yáñez, Camila Bontá, Carlos Torres-Herrera, Angela Garcia, Zorba Blázquez-Bermejo, Javier Castrodeza, Daniel Requena, Andreina Rodríguez, Arquimedes Silvio, Agustín Gatica, Arnulfo Begazo, Mario Alfaro

Faculty, Staff and Students Publications

AIMS: To evaluate the feasibility of a transthoracic echocardiogram using an apical-subcostal protocol in invasive mechanical ventilation (IMV) and prone position.

METHODS: Prospective study of adults who required a prone position during IMV. A pillow was placed only under the left hemithorax in the prone position to elevate and ease the apical and subcostal windows. A critical care cardiologist (prone group) acquired and evaluated the images using the apical-subcostal protocol. Besides, we used ambulatory echocardiograms performed as a comparative group (supine group).

RESULTS: 86 patients were included, 43 in the prone and 43 in the supine. In the prone group, …

Folate As A Potential Treatment For Lethal Ventricular Arrhythmias In Tango2-Deficiency Disorder, Weiyi Xu, Yingqiong Cao, Sara B Stephens, Maria Jose Arredondo, Yifan Chen, William Perez, Liang Sun, Andy C Yu, Jean J Kim, Seema R Lalani, Na Li, Frank T Horrigan, Francisco Altamirano, Xander Ht Wehrens, Christina Y Miyake, Lilei Zhang

Faculty, Staff and Students Publications

TANGO2-deficiency disorder (TDD) is an autosomal-recessive genetic disease caused by biallelic loss-of-function variants in the TANGO2 gene. TDD-associated cardiac arrhythmias are recalcitrant to standard antiarrhythmic medications and constitute the leading cause of death. Disease modeling for TDD has been primarily carried out using human dermal fibroblast and, more recently, in Drosophila by multiple research groups. No human cardiomyocyte system has been reported, which greatly hinders the investigation and understanding of TDD-associated arrhythmias. Here, we established potentially novel patient-derived induced pluripotent stem cell differentiated cardiomyocyte (iPSC-CM) models that recapitulate key electrophysiological abnormalities in TDD. These electrophysiological abnormalities were rescued in iPSC-CMs …

Genetic Alchemy Unveiled: Microrna-Mediated Gene Therapy As The Artisan Craft In The Battlefront Against Hepatocellular Carcinoma—A Comprehensive Chronicle Of Strategies And Innovations, Abduh Murshed, Mohammed A.H. Alnoud, Saleem Ahmad, Safir Ullah Khan, Mohammed Alissa, Meshari A. Alsuwat, Ahmed Ezzat Ahmed, Munir Ullah Khan

School of Graduate Studies Faculty Publications

Investigating therapeutic miRNAs is a rewarding endeavour for pharmaceutical companies. Since its discovery in 1993, our understanding of miRNA biology has advanced significantly. Numerous studies have emphasised the disruption of miRNA expression in various diseases, making them appealing candidates for innovative therapeutic approaches. Hepatocellular carcinoma (HCC) is a significant malignancy that poses a severe threat to human health, accounting for approximately 70%–85% of all malignant tumours. Currently, the efficacy of several HCC therapies is limited. Alterations in various biomacromolecules during HCC progression and their underlying mechanisms provide a basis for the investigation of novel and effective therapeutic approaches. MicroRNAs, also …

Protein Nanoparticles As Vaccine Platforms For Human And Zoonotic Viruses, Kush Kumar Pandey, Bikash R. Sahoo, Asit K. Pattnaik

Nebraska Center for Virology: Faculty Publications

Vaccines are one of the most effective medical interventions, playing a pivotal role in treating infectious diseases. Although traditional vaccines comprise killed, inactivated, or liveattenuated pathogens that have resulted in protective immune responses, the negative consequences of their administration have been well appreciated. Modern vaccines have evolved to contain purified antigenic subunits, epitopes, or antigen-encoding mRNAs, rendering them relatively safe. However, reduced humoral and cellular responses pose major challenges to these subunit vaccines. Protein nanoparticle (PNP)-based vaccines have garnered substantial interest in recent years for their ability to present a repetitive array of antigens for improving immunogenicity and enhancing protective …

Determining The Optimal Dosage Of Dexmedetomidine For Smooth Emergence In Older Patients Undergoing Spinal Surgery: A Study Of 44 Cases, Hyoeun Ahn, Yun Jeong Chae, Gyu Bin Choi, Min Gyu Lee, Ji Young Yoo

Faculty, Staff and Student Publications

BACKGROUND Emergence agitation, or delirium, occurs during early recovery from general anesthesia and involves disorientation, excitation, and uncontrolled physical movements. Dexmedetomidine is an alpha agonist that has sedative, anxiolytic, analgesic, and sympatholytic activities and is used as a continuous infusion to prevent emergence agitation. This study aimed to evaluate patients aged 65 years and older undergoing general anesthesia to determine the 90% effective dose (ED90) of dexmedetomidine continuous intraoperative infusion to prevent emergence agitation. MATERIAL AND METHODS We enrolled 44 patients aged 65 years and older undergoing spinal surgery under general anesthesia. Dexmedetomidine administration commenced 30 minutes before surgery completion, …

The Emerging Biomarkers In Chronic Obstructive Pulmonary Disease: A Narrative Review, Kaitlin M Phillips, Philip F Lavere, Nicola A Hanania, Muhammad Adrish

Faculty, Staff and Students Publications

The burden of chronic obstructive pulmonary disease (COPD) is increasing, especially for women in low-to-middle income countries. Biomarkers provide ever-increasing diagnostic precision for COPD and show promise for primary, secondary, and tertiary disease prevention. This review describes emerging applications for biomarkers in COPD, especially as they align with the Global Initiative for Chronic Obstructive Lung Disease (GOLD) emphasis on prevention, early diagnosis, and response to therapy. These biomarkers include blood eosinophils; IgE; C-reactive protein; fibrinogen; procalcitonin; interleukins 6, 8, and 33; tumor necrosis factor alpha; and soluble receptor for advanced glycated products (sRAGE). They have been used in various ways …

Feasibility Of Achieving Nutritional Adequacy In Critically Ill Children With Critical Neurological Illnesses (Cnis)?-A Quaternary Hospital Experience, Marwa Mansour, Nicole Knebusch, Jennifer Daughtry, Thomas P Fogarty, Fong Wilson Lam, Renan A Orellana, Yi-Chen Lai, Jennifer Erklauer, Jorge A Coss-Bu

Faculty, Staff and Students Publications

The literature on the nutritional needs and outcomes of critically ill children is scarce, especially on those with critical neurological illnesses (CNIs). Current evidence shows a lower mortality in patients who achieve two-thirds of their nutritional needs during the first week of pediatric intensive care unit (PICU) admission. We hypothesized that achieving 60% of the recommended dietary intake during the first week of a PICU stay is not feasible in patients with CNI. We designed an observational retrospective cohort study where we included all index admissions to the PICU in our institution of children (1 month to 18 years) with …

Community-Acquired Pneumonia: The Importance Of The Early Detection Of Drug-Resistant Organisms, Sai Doppalapudi, Muhammad Adrish

Faculty, Staff and Students Publications

Pneumonia is a disease associated with significant healthcare burden with over 1.5 million hospitalizations annually and is the eighth leading cause of death in the United States. While community-acquired pneumonia (CAP) is generally considered an acute time-limited illness, it is associated with high long-term mortality, with nearly one-third of patients requiring hospitalization dying within one year. An increasing trend of detecting multidrug-resistant (MDR) organisms causing CAP has been observed, especially in the Western world. In this editorial, we discuss about a publication by Jatteppanavar

Driving Pressure Decoded: Precision Strategies In Adult Respiratory Distress Syndrome Management, Muhammad Adrish, Sai Doppalapudi, Dmitry Lvovsky

Faculty, Staff and Students Publications

Mechanical ventilation (MV) is an important strategy for improving the survival of patients with respiratory failure. However, MV is associated with aggravation of lung injury, with ventilator-induced lung injury (VILI) becoming a major concern. Thus, ventilation protection strategies have been developed to minimize complications from MV, with the goal of relieving excessive breathing workload, improving gas exchange, and minimizing VILI. By opting for lower tidal volumes, clinicians seek to strike a balance between providing adequate ventilation to support gas exchange and preventing overdistension of the alveoli, which can contribute to lung injury. Additionally, other factors play a role in optimizing …

The Impact Of Mechanical Thrombectomy On The Blood-Brain Barrier In Patients With Acute Ischemic Stroke: A Non-Contrast Mr Imaging Study Using Dp-Pcasl And Noddi, Nikolaos Mouchtouris, Isaiah Ailes, Ki Chang, Adam Flanders, Feroze Mohamed, Stavropoula Tjoumakaris, Michael Gooch, Pascal Jabbour, Robert Rosenwasswer, Mahdi Alizadeh

Department of Neurosurgery Faculty Papers

Background and purpose: While mechanical thrombectomy (MT) achieves restoration of cerebral blood flow to the area at risk in patients with acute ischemic stroke (AIS), the influx of blood flow may exacerbate the blood-brain barrier (BBB) disruption and extravasation across the BBB, and it therefore remains unclear how reperfusion impacts the blood-brain barrier integrity. In this study, we use diffusion-prepared pseudocontinuous ASL (DP-pCASL) and Neurite Orientation Dispersion and Density Imaging (NODDI) sequence to measure the water exchange rate (k_w) in patients who underwent either MT or medical management and determine its impact on the brain tissue microstructure in …

Artificial Intelligence-Based Epigenomic, Transcriptomic And Histologic Signatures Of Tobacco Use In Oral Squamous Cell Carcinoma, Chi T Viet, Kesava R Asam, Gary Yu, Emma C Dyer, Sara Kochanny, Carissa M Thomas, Nicholas F Callahan, Anthony B Morlandt, Allen C Cheng, Ashish A Patel, Dylan F Roden, Simon Young, James Melville, Jonathan Shum, Paul C Walker, Khanh K Nguyen, Stephanie N Kidd, Steve C Lee, Gretchen S Folk, Dan T Viet, Anupama Grandhi, Jeremy Deisch, Yi Ye, Fatemeh Momen-Heravi, Alexander T Pearson, Bradley E Aouizerat

Faculty, Staff and Student Publications

Oral squamous cell carcinoma (OSCC) biomarker studies rarely employ multi-omic biomarker strategies and pertinent clinicopathologic characteristics to predict mortality. In this study we determine for the first time a combined epigenetic, gene expression, and histology signature that differentiates between patients with different tobacco use history (heavy tobacco use with ≥10 pack years vs. no tobacco use). Using The Cancer Genome Atlas (TCGA) cohort (n = 257) and an internal cohort (n = 40), we identify 3 epigenetic markers (GPR15, GNG12, GDNF) and 13 expression markers (IGHA2, SCG5, RPL3L, NTRK1, CD96, BMP6, TFPI2, EFEMP2, RYR3, DMTN, GPD2, BAALC, and FMO3), which …

Application Of Simultaneous Uncertainty Quantification And Segmentation For Oropharyngeal Cancer Use-Case With Bayesian Deep Learning, Jaakko Sahlsten, Joel Jaskari, Kareem A Wahid, Sara Ahmed, Enrico Glerean, Renjie He, Benjamin H Kann, Antti Mäkitie, Clifton D Fuller, Mohamed A Naser, Kimmo Kaski

Faculty, Staff and Student Publications

BACKGROUND: Radiotherapy is a core treatment modality for oropharyngeal cancer (OPC), where the primary gross tumor volume (GTVp) is manually segmented with high interobserver variability. This calls for reliable and trustworthy automated tools in clinician workflow. Therefore, accurate uncertainty quantification and its downstream utilization is critical.

METHODS: Here we propose uncertainty-aware deep learning for OPC GTVp segmentation, and illustrate the utility of uncertainty in multiple applications. We examine two Bayesian deep learning (BDL) models and eight uncertainty measures, and utilize a large multi-institute dataset of 292 PET/CT scans to systematically analyze our approach.

RESULTS: We show that our uncertainty-based approach …

Novel Human Recombinant N-Acetylgalactosamine-6-Sulfate Sulfatase Produced In A Glyco-Engineered Escherichia Coli Strain, Luisa N. Pimentel-Vera, Alexander Rodríguez-López, Angela J. Espejo-Mojica, Aura María Ramírez, Carolina Cardona, Luis H. Reyes, Shunji Tomatsu, Thapakorn Jaroentomeechai, Matthew P. Delisa, Oscar F. Sánchez, Carlos J. Alméciga-Díaz

Department of Pediatrics Faculty Papers

Mucopolysaccharidosis IVA (MPS IVA) is a lysosomal storage disease caused by mutations in the gene encoding the lysosomal enzyme N-acetylgalactosamine-6-sulfate sulfatase (GALNS), resulting in the accumulation of keratan sulfate (KS) and chondroitin-6-sulfate (C6S). Previously, it was reported the production of an active human recombinant GALNS (rGALNS) in E. coli BL21(DE3). However, this recombinant enzyme was not taken up by HEK293 cells or MPS IVA skin fibroblasts. Here, we leveraged a glyco-engineered E. coli strain to produce a recombinant human GALNS bearing the eukaryotic trimannosyl core N-glycan, Man3GlcNAc2 (rGALNSoptGly). The N-glycosylated GALNS was produced at 100 …

Early Outcomes Of Transcatheter Aortic Valve Implantation With Next-Generation Balloon-Expandable Myval Transcatheter Heart Valve: Single-Center Experience From Iraq, Khalid Ibrahim Amber, Ammar Jabbar Majeed

Journal of the Saudi Heart Association

Objectives: Transcatheter aortic valve implantation (TAVI) is a minimally invasive percutaneous procedure for the treatment of elderly patients with symptomatic severe aortic stenosis. The study aimed to determine immediate (in-hospital) and short-term (30-day) outcomes of TAVI with next-generation balloon-expandable Myval transcatheter heart valve (THV) at a single-centre in Iraq. Methods: During January 2019 to January 2024, a total of 100 symptomatic severe aortic stenosis patients who underwent TAVI using Myval THV at Al-Najaf Cardiac Center, Iraq were enrolled. The procedure was done under local anesthesia and conscious sedation via transfemoral approach, using balloon-expandable Myval THV. All patients were followed-up at …