Medicine and Health Sciences Commons^™

Usf Jamovi Tutorial Project: Open Education Resource, Aline Hitti, Saera Khan

USF OER Faculty Grant

Jamovi is an open source free software that USF staff, faculty and student can download to carry out any statistical analyses. The current report summarizes the progress made on an Open Education Resource Grant funded project, which aimed to created Jamovi tutorials. In this report, student feedback and faculty reaction are summarized after one semester of using the tutorials created.

Biologic Tnf-Α Inhibitors Reduce Microgliosis, Neuronal Loss, And Tau Phosphorylation In A Transgenic Mouse Model Of Tauopathy, Weijun Ou, Joshua Yang, Juste Simanauskaite, Matthew Choi, Demi M. Castellanos, Rudy Chang, Jiahong Sun, Nataraj Jagadeesan, Karen D. Parfitt, David H. Cribbs, Rachita K. Sumbria

Pharmacy Faculty Articles and Research

Background

Tumor necrosis factor-α (TNF-α) plays a central role in Alzheimer’s disease (AD) pathology, making biologic TNF-α inhibitors (TNFIs), including etanercept, viable therapeutics for AD. The protective effects of biologic TNFIs on AD hallmark pathology (Aβ deposition and tau pathology) have been demonstrated. However, the effects of biologic TNFIs on Aβ-independent tau pathology have not been reported. Existing biologic TNFIs do not cross the blood–brain barrier (BBB), therefore we engineered a BBB-penetrating biologic TNFI by fusing the extracellular domain of the type-II human TNF-α receptor (TNFR) to a transferrin receptor antibody (TfRMAb) that ferries the TNFR into the brain via …

Nutritional Status Of Children Living Within Institution-Based Care: A Retrospective Analysis With Funnel Plots And Control Charts For Programme Monitoring, Emily Delacey, Evan Hilberg, Elizabeth Allen, Michael Quiring, Cally J. Tann, Nora Ellen Groce, James Vilus, Ethan A. Bergman, Merzel Demasu-Ay, Hang T. Dam, Marko Kerac

All Faculty Scholarship for the College of Education and Professional Studies

Objectives The aim of this study is to fill a key information gap on the nutrition-related epidemiology of orphaned and vulnerable children living within institution-based care (IBC) across six countries.

Design A retrospective analysis with Shewhart control charts and funnel plots to explore intersite and over time variations in nutritional status.

Setting We conducted a retrospective analysis of records from Holt International’s Child Nutrition Programme from 35 sites in six countries; Mongolia, India, Ethiopia, Vietnam, China and the Philippines.

Participants Deidentified health records from Holt International’s online nutrition screening database included records from 2926 children, 0–18 years old. Data were …

Inhibition Of Bruton Tyrosine Kinase Reduces Neuroimmune Cascade And Promotes Recovery After Spinal Cord Injury, Chen Guang Yu, Vimala Bondada, Hina Iqbal, Kate L. Moore, John C. Gensel, Subbarao Bondada, James W. Geddes

Physiology Faculty Publications

Microglia/astrocyte and B cell neuroimmune responses are major contributors to the neurological deficits after traumatic spinal cord injury (SCI). Bruton tyrosine kinase (BTK) activation mechanistically links these neuroimmune mechanisms. Our objective is to use Ibrutinib, an FDA-approved BTK inhibitor, to inhibit the neuroimmune cascade thereby improving locomotor recovery after SCI. Rat models of contusive SCI, Western blot, immunofluorescence staining imaging, flow cytometry analysis, histological staining, and behavioral assessment were used to evaluate BTK activity, neuroimmune cascades, and functional outcomes. Both BTK expression and phosphorylation were increased at the lesion site at 2, 7, 14, and 28 days after SCI. Ibrutinib …

Novel Biomarkers Of Ciliary Extracellular Vesicles Interact With Ciliopathy And Alzheimer’S Associated Proteins, Ashraf M. Mohieldin, Amal Alachkar, John R. Yates Iii, Surya M. Nauli

Pharmacy Faculty Articles and Research

Ciliary extracellular vesicles (ciEVs), released from primary cilia, contain functional proteins that play an important role in cilia structure and functions. We have recently shown that ciEVs and cytosolic extracellular vesicles (cyEVs) have unique and distinct biomarkers. While ciEV biomarkers have shown some interactions with known ciliary proteins, little is known about the interaction of ciEV proteins with proteins involved in ciliopathy and neurodegenerative disorders. Here, we reveal for the first time the protein-protein interaction (PPI) between the top five ciEVs biomarkers with ciliopathy and Alzheimer disease (AD) proteins. These results support the growing evidence of the critical physiological roles …

Likely Community Transmission Of Covid-19 Infections Between Neighboring, Persistent Hotspots In Ontario, Canada, Ben C. Shirley, Eliseos J. Mucaki, Peter Rogan

Biochemistry Publications

Introduction: This study aimed to produce community-level geo-spatial mapping of confirmed COVID-19 cases in Ontario Canada in near real-time to support decision-making. This was accomplished by area-to-area geostatistical analysis, space-time integration, and spatial interpolation of COVID-19 positive individuals.
Methods: COVID-19 cases and locations were curated for geostatistical analyses from March 2020 through June 2021, corresponding to the first, second, and third waves of infections. Daily cases were aggregated according to designated forward sortation area (FSA), and postal codes (PC) in municipal regions Hamilton, Kitchener/Waterloo, London, Ottawa, Toronto, and Windsor/Essex county. Hotspots were identified with area-to-area tests including Getis-Ord Gi*, Global …

Adipose-Specific Pparα Knockout Mice Have Increased Lipogenesis By Pask–Srebp1 Signaling And A Polarity Shift To Inflammatory Macrophages In White Adipose Tissue, Terry D. Hinds, Jr., Zachary A. Kipp, Mei Xu, Frederique B. Yiannikouris, Andrew J. Morris, Donald F. Stec, Walter Wahli, David E. Stec

Pharmacology and Nutritional Sciences Faculty Publications

The nuclear receptor PPARα is associated with reducing adiposity, especially in the liver, where it transactivates genes for β-oxidation. Contrarily, the function of PPARα in extrahepatic tissues is less known. Therefore, we established the first adipose-specific PPARα knockout (Ppara^FatKO) mice to determine the signaling position of PPARα in adipose tissue expansion that occurs during the development of obesity. To assess the function of PPARα in adiposity, female and male mice were placed on a high-fat diet (HFD) or normal chow for 30 weeks. Only the male Ppara^FatKO animals had significantly more adiposity in the inguinal white …

Genetic Contributors Of Incident Stroke In 10,700 African Americans With Hypertension: A Meta-Analysis From The Genetics Of Hypertension Associated Treatments And Reasons For Geographic And Racial Differences In Stroke Studies, Nicole D. Armstrong, Vinodh Srinivasasainagendra, Amit Patki, Rikki M. Tanner, Bertha A. Hidalgo, Hemant K. Tiwari, Nita A. Limdi, Ethan M. Lange, Leslie A. Lange, Donna K. Arnett, Marguerite R. Irvin

Epidemiology and Environmental Health Faculty Publications

Background: African Americans (AAs) suffer a higher stroke burden due to hypertension. Identifying genetic contributors to stroke among AAs with hypertension is critical to understanding the genetic basis of the disease, as well as detecting at-risk individuals.

Methods: In a population comprising over 10,700 AAs treated for hypertension from the Genetics of Hypertension Associated Treatments (GenHAT) and Reasons for Geographic and Racial Differences in Stroke (REGARDS) studies, we performed an inverse variance-weighted meta-analysis of incident stroke. Additionally, we tested the predictive accuracy of a polygenic risk score (PRS) derived from a European ancestral population in both GenHAT and REGARDS AAs …

Late-Life Exercise Mitigates Skeletal Muscle Epigenetic Aging, Kevin A. Murach, Andrea L. Dimet-Wiley, Yuan Wen, Camille R. Brightwell, Christine M. Latham, Cory M. Dungan, Christopher S. Fry, Stanley J. Watowich

Center for Muscle Biology Faculty Publications

There are functional benefits to exercise in muscle, even when performed late in life, but the contributions of epigenetic factors to late-life exercise adaptation are poorly defined. Using reduced representation bisulfite sequencing (RRBS), ribosomal DNA (rDNA) and mitochondrial-specific examination of methylation, targeted high-resolution methylation analysis, and DNAge™ epigenetic aging clock analysis with a translatable model of voluntary murine endurance/resistance exercise training (progressive weighted wheel running, PoWeR), we provide evidence that exercise may mitigate epigenetic aging in skeletal muscle. Late-life PoWeR from 22–24 months of age modestly but significantly attenuates an age-associated shift toward promoter hypermethylation. The epigenetic age of muscle …

Cryptococcus Neoformans Melanization Incorporates Multiple Catecholamines To Produce Polytypic Melanin, Rosanna P. Baker, Christine Chrissian, Ruth E. Stark, Arturo Casadevall

Publications and Research

Melanin is a major virulence factor in pathogenic fungi that enhances the ability of fungal cells to resist immune clearance. Cryptococcus neoformans is an important human pathogenic fungus that synthesizes melanin from exogenous tissue catecholamine precursors during infection, but the type of melanin made in cryptococcal meningoencephalitis is unknown. We analyzed the efficacy of various catecholamines found in brain tissue in supporting melanization using animal brain tissue and synthetic catecholamine mixtures reflecting brain tissue proportions. Solid-state NMR spectra of the melanin pigment produced from such mixtures yielded more melanin than expected if only the preferred constituent dopamine had been incorporated, …

A Protocol For Rapid And Parallel Isolation Of Myocytes And Non-Myocytes From Multiple Mouse Hearts., Gabriella E Farrugia, Michael A Mclellan, Kate L Weeks, Aya Matsumoto, Charles D Cohen, Crisdion Krstevski, Taylah L Gaynor, Adam C Parslow, Julie R Mcmullen, Alexander R Pinto

Faculty Research 2021

This protocol features parallel isolation of myocytes and non-myocytes from murine hearts. It was designed with considerations for (1) time required to extract cardiac cells, (2) cell viability, and (3) protocol scalability. Here, a peristaltic pump and 3D-printed elements are combined to perfuse the heart with enzymes to dissociate cells. Myocytes and non-myocytes extracted using this protocol are separated by centrifugation and/or fluorescence-activated cell sorting for use in downstream applications including single-cell omics or other bio-molecular analyses. For complete details on the use and execution of this protocol, please refer to McLellan et al. (2020).

Measuring Science Teachers' Emotional Experiences With Evolution Using Real World Scenarios, William Lee Romine, Rutuja Mahajan, Amber Todd

Biological Sciences Faculty Publications

Low acceptance of evolution remains an obstacle to quality biology instruction. We develop and utilize a novel assessment which measures emotional experience in light of real-world evolution education scenarios. We presented 296 science teachers 4 pro-evolution and 8 anti-evolution scenarios and asked them to rate their levels of joy, anger, sadness, fear, disgust, shame, and guilt elicited by that scenario on an ordinal 5-point scale. We used exploratory factor analysis to extract the most important dimensions in the teachers’ responses, Rasch analysis to explore the validity of the extracted subscales, and stepwise regression to find the most important factors driving …

Nuclear Pore Protein Nup210 Depletion Suppresses Metastasis Through Heterochromatin-Mediated Disruption Of Tumor Cell Mechanical Response., Ruhul Amin, Anjali Shukla, Jacqueline Jufen Zhu, Sohyoung Kim, Ping Wang, Simon Zhongyuan Tian, Andy D Tran, Debasish Paul, Steven D Cappell, Sandra Burkett, Huaitian Liu, Maxwell P Lee, Michael J Kruhlak, Jennifer E Dwyer, R Mark Simpson, Gordon L Hager, Yijun Ruan, Kent W Hunter

Faculty Research 2021

Mechanical signals from the extracellular microenvironment have been implicated in tumor and metastatic progression. Here, we identify nucleoporin NUP210 as a metastasis susceptibility gene for human estrogen receptor positive (ER+) breast cancer and a cellular mechanosensor. Nup210 depletion suppresses lung metastasis in mouse models of breast cancer. Mechanistically, NUP210 interacts with LINC complex protein SUN2 which connects the nucleus to the cytoskeleton. In addition, the NUP210/SUN2 complex interacts with chromatin via the short isoform of BRD4 and histone H3.1/H3.2 at the nuclear periphery. In Nup210 knockout cells, mechanosensitive genes accumulate H3K27me3 heterochromatin modification, mediated by the polycomb repressive complex 2 …

Visualizing Phytochemical-Protein Interaction Networks: Momordica Charantia And Cancer, Yumi L. Briones, Alexander T. Young, Fabian M. Dayrit, Armando Jerome De Jesus, Nina Rosario L. Rojas

Chemistry Faculty Publications

The in silico study of medicinal plants is a rapidly growing field. Techniques such as reverse screening and network pharmacology are used to study the complex cellular action of medicinal plants against disease. However, it is difficult to produce a meaningful visualization of phytochemical-protein interactions (PCPIs) in the cell. This study introduces a novel workflow combining various tools to visualize a PCPI network for a medicinal plant against a disease. The five steps are 1) phytochemical compilation, 2) reverse screening, 3) network building, 4) network visualization, and 5) evaluation. The output is a PCPI network that encodes multiple dimensions of …

Improving Care For Patients With Atrial Fibrillation Through The Use Of A Personal Electrocardiogram, Teresa Praus, Jonathan Li, Svetlana Barbarash, Manuel Proenza, Mary D. Bondmass

Nursing Faculty Publications

Background: Atrial fibrillation (AF) is the most common arrhythmia affecting more than six million people in the United States. The economic burden is estimated to be >$6 billion annually with catastrophic events dramatically increasing expenditure. When patients experience symptoms, they commonly present to an acute care facility; this can be costly and anxiety provoking. Local problem: Same-day access issues prohibit patients from communicating directly with their cardiology provider, forcing them to use resources and increasing psychological burden.Methods:A convenience sample, made up of 43 patients, was given a KardiaMobile device. Eligible patients had ≥2 AF-related emergency department (ED) or urgent care …

Evidence Of Myomir Regulation Of The Pentose Phosphate Pathway During Mechanical Load-Induced Hypertrophy, Taylor Valentino, Vandre C. Figueiredo, C. Brooks Mobley, John J. Mccarthy, Ivan J. Vechetti Jr.

Physiology Faculty Publications

Many of the molecular and cellular mechanisms discovered to regulate skeletal muscle hypertrophy were first identified using the rodent synergist ablation model. This model reveals the intrinsic capability and necessary pathways of skeletal muscle growth in response to mechanical overload (MOV). Reminiscent of the rapid cellular growth observed with cancer, we hypothesized that in response to MOV, skeletal muscle would undergo metabolic programming to sustain increased demands to support hypertrophy. To test this hypothesis, we analyzed the gene expression of specific metabolic pathways taken from transcriptomic microarray data of a MOV time course. We found an upregulation of genes involved …

Meta-Analyses Identify Dna Methylation Associated With Kidney Function And Damage, Pascal Schlosser, Adrienne Tin, Pamela R Matias-Garcia, Chris H L Thio, Roby Joehanes, Hongbo Liu, Antoine Weihs, Zhi Yu, Anselm Hoppmann, Franziska Grundner-Culemann, Josine L Min, Adebowale A Adeyemo, Charles Agyemang, Johan Ärnlöv, Nasir A Aziz, Andrea Baccarelli, Murielle Bochud, Hermann Brenner, Monique M B Breteler, Cristian Carmeli, Layal Chaker, John C Chambers, Shelley A Cole, Josef Coresh, Tanguy Corre, Adolfo Correa, Simon R Cox, Niek De Klein, Graciela E Delgado, Arce Domingo-Relloso, Kai-Uwe Eckardt, Arif B Ekici, Karlhans Endlich, Kathryn L Evans, James S Floyd, Myriam Fornage, Lude Franke, Eliza Fraszczyk, Xu Gao, Xīn Gào, Mohsen Ghanbari, Sahar Ghasemi, Christian Gieger, Philip Greenland, Megan L Grove, Sarah E Harris, Gibran Hemani, Peter Henneman, Christian Herder, Steve Horvath, Lifang Hou, Mikko A Hurme, Shih-Jen Hwang, Marjo-Riitta Jarvelin, Sharon L R Kardia, Silva Kasela, Marcus E Kleber, Wolfgang Koenig, Jaspal S Kooner, Holly Kramer, Florian Kronenberg, Brigitte Kühnel, Terho Lehtimäki, Lars Lind, Dan Liu, Yongmei Liu, Donald M Lloyd-Jones, Kurt Lohman, Stefan Lorkowski, Ake T Lu, Riccardo E Marioni, Winfried März, Daniel L Mccartney, Karlijn A C Meeks, Lili Milani, Pashupati P Mishra, Matthias Nauck, Ana Navas-Acien, Christoph Nowak, Annette Peters, Holger Prokisch, Bruce M Psaty, Olli T Raitakari, Scott M Ratliff, Alex P Reiner, Sylvia E Rosas, Ben Schöttker, Joel Schwartz, Sanaz Sedaghat, Jennifer A Smith, Nona Sotoodehnia, Hannah R Stocker, Silvia Stringhini, Johan Sundström, Brenton R Swenson, Maria Tellez-Plaza, Joyce B J Van Meurs, Jana V Van Vliet-Ostaptchouk, Andrea Venema, Niek Verweij, Rosie M Walker, Matthias Wielscher, Juliane Winkelmann, Bruce H R Wolffenbuttel, Wei Zhao, Yinan Zheng, Marie Loh, Harold Snieder, Daniel Levy, Melanie Waldenberger, Katalin Susztak, Anna Köttgen, Alexander Teumer

Journal Articles

Chronic kidney disease is a major public health burden. Elevated urinary albumin-to-creatinine ratio is a measure of kidney damage, and used to diagnose and stage chronic kidney disease. to extend the knowledge on regulatory mechanisms related to kidney function and disease, we conducted a blood-based epigenome-wide association study for estimated glomerular filtration rate (n = 33,605) and urinary albumin-to-creatinine ratio (n = 15,068) and detected 69 and seven CpG sites where DNA methylation was associated with the respective trait. The majority of these findings showed directionally consistent associations with the respective clinical outcomes chronic kidney disease and moderately increased albuminuria. …

Age And Not The Preferred Limb Influences The Kinematic Structure Of Pointing Movements, Kurt W. Kornatz, Brach Poston, George E. Stelmach

Kinesiology and Nutrition Sciences Faculty Publications

In goal-directed movements, effective open-loop control reduces the need for feedback-based corrective submovements. The purpose of this study was to determine the influence of hand preference and aging on submovements during single-and two-joint pointing movements. A total of 12 young and 12 older right-handed participants performed pointing movements that involved either elbow extension or a combination of elbow extension and horizontal shoulder flexion with their right and left arms to a target. Kinematics were used to separate the movements into their primary and secondary submovements. The older adults exhibited slower movements, used secondary submovements more often, and produced relatively shorter …

Ketone Body Metabolism In The Ischemic Heart, Stephen C. Kolwicz Jr.

Health and Exercise Physiology Faculty Publications

Ketone bodies have been identified as an important, alternative fuel source in heart failure. In addition, the use of ketone bodies as a fuel source has been suggested to be a potential ergogenic aid for endurance exercise performance. These findings have certainly renewed interest in the use of ketogenic diets and exogenous supplementation in an effort to improve overall health and disease. However, given the prevalence of ischemic heart disease and myocardial infarctions, these strategies may not be ideal for individuals with coronary artery disease. Although research studies have clearly defined changes in fatty acid and glucose metabolism during ischemia …

Keratin 1 As A Cell-Surface Receptor In Cancer, Oluseye Ogunnigbagbe, Christopher G. Bunick, Kamaljit Kaur

Pharmacy Faculty Articles and Research

Keratins are fibrous proteins that take part in several important cellular functions, including the formation of intermediate filaments. In addition, keratins serve as epithelial cell markers, which has made their role in cancer progression, diagnosis, and treatment an important focus of research. Keratin 1 (K1) is a type II keratin whose structure is comprised of a coiled-coil central domain flanked by flexible, glycine-rich loops in the N- and C-termini. While the structure of cytoplasmic K1 is established, the structure of cell-surface K1 is not known. Several transformed cells, such as cancerous cells and cells that have undergone oxidative stress, display …

The Effect Of Twist1b And Twist2 Knockdown On Tgf-Beta Signaling Expression In Tendon Progenitors, Marinia N. Bishay

Honors Scholars Collaborative Projects

Somites are important mesoderm structures that form in regularly timed intervals from the anterior end of the paraxial mesoderm at the end of gastrulation during embryogenesis. Cells of the ventromedial portion of the somite, the sclerotome, undergo epithelial to mesenchymal transition, surround the notochord, and give rise to connective tissues of the axial skeleton including the vertebrae, tendons, and ligaments. We are interested in understanding how the sclerotome is compartmentalized into the region that makes tendons. Genes expressed in the sclerotome, twist1 and twist2, are likely involved in the downstream differentiation of sclerotome to tendon progenitors. Previous studies have shown …

Hospital Effluents And Wastewaters Treatment Plants: A Source Of Oxytetracycline And Antimicrobial-Resistant Bacteria In Seafood, Bozena Mccarthy, Samuel Obeng Apori, Michelle Giltrap, Abhijnan Bhat, James Curtin, Furong Tian

Articles

The present study employs a data review on the presence and aggregation of oxytetracycline (OTC) and resistance (AMR) bacteria in wastewater treatment plants (WWTPs), and distribution of the contaminated effluent with the aid of shallow and deep ocean currents. The study aims to determine the fate of OTC, AMR bacteria in seafood, and demonstrate a relationship between AMR levels and human health. This review includes (1) OTC, (2) AMR bacteria, (3) heavy metals in aquatic environments, and their relationship. Few publications describe OCT in surface waters. Although, OTC and other tetracyclines were found in 10 countries in relatively low concentrations, …

Policy Implications Of The Covid-19 Pandemic On Food Security In Rural America: Evidence From Appalachia, Kathryn M. Cardarelli, Emily M. Dewitt, Rachel Gillespie, Rachel Hogg-Graham, Heather Norman-Burgdolf, Janet T. Mullins

Dietetics and Human Nutrition Faculty Publications

Rural communities are disproportionally affected by food insecurity, making them vulnerable to the consequences of supply disruptions caused by the COVID-19 pandemic. While access to food was initially diminished due to food supply disruptions, little is known about the mechanisms through which federal emergency assistance programs impacted food access in rural populations. Through a series of five focus groups in spring 2021, we examined the impact of the COVID-19 pandemic on food access in a rural Appalachian community in Kentucky. Data were analyzed using a Grounded Theory Approach. Findings revealed the following four primary themes: food scarcity in grocery stores; …

Bile Acid Profiling Reveals Distinct Signatures In Undernourished Children With Environmental Enteric Dysfunction, Xueheng Zhao, Kenneth D R. Setchell, Rong Huang, Indika Mallawaarachchi, Lubaina Ehsan, Edward Dobrzykowski Iii, Junfang Zhao, Sana Syed, Najeeha Talat Iqbal, Junaid Iqbal, Kamran Sadiq, Sheraz Ahmed, Syed Asad Ali

Department of Paediatrics and Child Health

Background: Intestinal inflammation and malabsorption in environmental enteric dysfunction (EED) are associated with early childhood growth faltering in impoverished settings worldwide.
Objectives: The goal of this study was to identify candidate biomarkers associated with inflammation, EED histology, and as predictors of later growth outcomes by focusing on the liver-gut axis by investigating the bile acid metabolome.
Methods: Undernourished rural Pakistani infants (n = 365) with weight-for-height Z score (WHZ) < -2 were followed up to the age of 24 mo and monitored for growth, infections, and EED. Well-nourished local children (n = 51) were controls, based on consistent WHZ > 0 and height-for-age Z score (HAZ) > -1 on 2 consecutive visits at 3 and 6 mo. Serum bile acid (sBA) profiles were measured by tandem MS at the ages of 3-6 …

Novel Approaches For Enhancing Cell Survival And Function In Vivo, Ou Wang

Department of Chemical and Biomolecular Engineering: Theses and Student Research

FDA has approved several cell-based therapeutics and hundreds of cell therapy clinical trials are ongoing. Cells will be a significant type of medicine after small molecule and protein drugs. However, several obstacles need to be addressed to achieve the widespread use of cellular therapeutics. The first challenge is the low efficacy of cell transplantation due to low retention, survival, integration, and function of cells in vivo. The second challenge is producing a massive number of cells for clinical treatment with cost-effectively and reproducibly technologies.

In this thesis, we proposed and investigated two approaches to address these challenges. To begin …

A Dystrophin Exon‐52 Deleted Miniature Pig Model Of Duchenne Muscular Dystrophy And Evaluation Of Exon Skipping, Yusuke Echigoya, Nhu Trieu, William Duddy, Hong M. Moulton, Haifang Yin, Terence A. Partridge, Eric P. Hoffman, Joe N. Kornegay, Frank A. Rohret, Christopher S. Rogers, Toshifumi Yokota

Genomics and Precision Medicine Faculty Publications

No abstract provided.

Supervised Learning With Word Embeddings Derived From Pubmed Captures Latent Knowledge About Protein Kinases And Cancer., Vida Ravanmehr, Hannah Blau, Luca Cappelletti, Tommaso Fontana, Leigh Carmody, Ben D Coleman, Joshy George, Justin Reese, Marcin Joachimiak, Giovanni Bocci, Peter Hansen, Carol J Bult, Jens Rueter, Elena Casiraghi, Giorgio Valentini, Christopher Mungall, Tudor I Oprea, Peter N Robinson

Faculty Research 2021

Inhibiting protein kinases (PKs) that cause cancers has been an important topic in cancer therapy for years. So far, almost 8% of >530 PKs have been targeted by FDA-approved medications, and around 150 protein kinase inhibitors (PKIs) have been tested in clinical trials. We present an approach based on natural language processing and machine learning to investigate the relations between PKs and cancers, predicting PKs whose inhibition would be efficacious to treat a certain cancer. Our approach represents PKs and cancers as semantically meaningful 100-dimensional vectors based on word and concept neighborhoods in PubMed abstracts. We use information about phase …

Core-Atac: A Deep Learning Model For The Functional Classification Of Regulatory Elements From Single Cell And Bulk Atac-Seq Data., Asa Thibodeau, Shubham Khetan, Alper Eroglu, Ryan Tewhey, Michael L. Stitzel, Duygu Ucar

Faculty Research 2021

Cis-Regulatory elements (cis-REs) include promoters, enhancers, and insulators that regulate gene expression programs via binding of transcription factors. ATAC-seq technology effectively identifies active cis-REs in a given cell type (including from single cells) by mapping accessible chromatin at base-pair resolution. However, these maps are not immediately useful for inferring specific functions of cis-REs. For this purpose, we developed a deep learning framework (CoRE-ATAC) with novel data encoders that integrate DNA sequence (reference or personal genotypes) with ATAC-seq cut sites and read pileups. CoRE-ATAC was trained on 4 cell types (n = 6 samples/replicates) and accurately predicted known cis-RE functions from …

Abdominal Computed Tomography Imaging Findings In Hospitalized Covid-19 Patients: A Year-Long Experience And Associations Revealed By Explainable Artificial Intelligence., Alice Scarabelli, Massimo Zilocchi, Elena Casiraghi, Pierangelo Fasani, Guido Giovanni Plensich, Andrea Alessandro Esposito, Elvira Stellato, Alessandro Petrini, Justin Reese, Peter N Robinson, Giorgio Valentini, Gianpaolo Carrafiello

Faculty Research 2021

The aim of this retrospective study is to assess any association between abdominal CT findings and the radiological stage of COVID-19 pneumonia, pulmonary embolism and patient outcomes. We included 158 adult hospitalized COVID-19 patients between 1 March 2020 and 1 March 2021 who underwent 206 abdominal CTs. Two radiologists reviewed all CT images. Pathological findings were classified as acute or not. A subset of patients with inflammatory pathology in ACE2 organs (bowel, biliary tract, pancreas, urinary system) was identified. The radiological stage of COVID pneumonia, pulmonary embolism, overall days of hospitalization, ICU admission and outcome were registered. Univariate statistical analysis …

Restructuring Training (Participation House Support Services), Victoria Lun, Do Yeon Oh, Nadir Saeed, Joe Thorne, Alexander Trusler

Medical Sciences 4300A: Addressing Healthcare Misconceptions Using Scientific Inquiry

Participation House Support Services (PHSS) is a non-profit organization with over 60 locations across Ontario that serves individuals with complex medical, physical, and developmental needs with the goal of including them in the community. The scope of the project covers members of the PHSS organization and the London community that they serve by addressing problems with burnout and culture of resentment that the Coordinators of the organization face. After initial discussions with the community partner, qualitative research was done via focus groups with PHSS Coordinators and training staff. An agreed-upon solution of restructuring the training process was developed, as training …