Digital Commons Network^™

Staff Education To Nurse Practitioners On Proper Std Treatment, Jolanda Monique Amey

Walden Dissertations and Doctoral Studies

This Doctor of Nursing Practice project implemented a structured staff education project to strengthen nurse practitioner knowledge related to the diagnosis and treatment of sexually transmitted diseases in a public health setting. Nurse practitioners often serve as the primary providers of sexually transmitted disease care for underserved and uninsured populations. Maintaining current knowledge of Centers for Disease Control and Prevention (CDC) treatment guidelines is essential to reducing reinfection, limiting transmission, and promoting safe, evidence-based care. When guideline knowledge is inconsistent or outdated, opportunities for appropriate treatment may be missed. The practice-focused question guiding this project was “Among nurse practitioners in …

Covid-19 Risky Health Behavior Among College Students, Azait Imtiaz

James Madison Undergraduate Research Journal (JMURJ)

This research explored the behavior of college students before and after the implementation of a mask mandate during the COVID-19 pandemic. A cross-sectional online survey was conducted at a public university in the Shenandoah Valley region of Virginia with 807 college students. The study assessed various factors, including living arrangements (shared living spaces such as rooms and bathrooms), social behavior (including social gatherings), adherence to mask protocols during gatherings, and hygiene practices (such as hand sanitization). The results indicated significant differences in social behavior (M_before = 19.82, M_after = 25.85, p =.001), mask-wearing (M_before = 20.73, M_after = 31.41, p …

Staff Education For Timely Sepsis Intervention At The Medical Center, Latonya Summers-Oliver

Walden Dissertations and Doctoral Studies

This project developed a staff education program to clarify the concept of “time zero,” essential for timely sepsis intervention, in alignment with the SEP-1 core measure by CMS, which prescribes evidence-based treatment bundles within specific time frames. Aiming to improve staff knowledge in sepsis identification, treatment, and management, the program incorporated a literature review supporting educational strategies that enhance mortality rates and clinical outcomes. Using pre- and posttest assessments, the study demonstrated significant improvements in staff knowledge following targeted education on sepsis recognition and timely management. The findings underscore the importance of standardized, accessible training programs to improve clinical response, …

Translating Social Accountability Values Into Practice: Doctors’ Experiences From Problem- Based Learning Medical Curriculum In The United Arab Emirates, Nihar Ranjan Dash, Ahmed Alrazzak Hasswan, Mayar Abbas Ahmed Essam Samaha, Kamel A. Samara, Mohamed Hassan Taha

Abington Jefferson Health Papers

Purpose: Medical schools play a crucial role in preparing future doctors to address the health needs of patients and their communities. Graduates are expected to provide socially accountable care by upholding values such as relevance, equity, quality, and cost- effectiveness. This study explores how these values are understood and applied by medical graduates trained in problem-based learning (PBL) curricula. Methods: A cross-sectional online survey was conducted among University of Sharjah medical graduates to assess their exposure to and practice of social accountability values. Results: Of the 689 graduates invited, 503 (73%) responded, including 329 (65%) women. Most respondents, 375 (75%), …

Zingiber Officinale-Mediated Zinc Oxide Nanoparticles: Antimicrobial Activity Against Multidrug-Resistant Bacteria, Maureen Bakor Tabe, Ovgu Isbilen, Jennifer N Walker, Ender Cinar

Faculty, Staff and Student Publications

Background: The fight against infectious diseases has transformed over the past century with the emergence of multidrug-resistant bacteria, where pathogens that exhibit resistance to multiple antibiotic classes leading to significant challenges to modern medicine. Zingiber officinale is well-documented to exhibit diverse biological activities, including strong antioxidant, antimicrobial, and anti-neuroinflammatory effects. Zinc oxide nanoparticles can be synthesized cost-effectively and are widely utilized in biomedical applications, including their use as anticancer agents and drug-delivery systems, as well as for their intrinsic antibacterial and anti-inflammatory properties. In this study, we aimed to take a combinatorial approach to investigate the antimicrobial effects of Z. …

Endothelial Oncogenic Kras Mutation Drives The Dynamics Of Microglia And Macrophages In Brain Arteriovenous Malformation, Hyejin Park, Jung-Eun Park, Bridger H Freeman, Bosco Seong Kyu Yang, Shun-Ming Ting, Alexander K Suh, Jude Pj Savarraj, Shuning Huang, Jakob Körbelin, Huimahn Alex Choi, Sean P Marrelli, Jaroslaw Aronowski, Peng Roc Chen, Eunhee Kim, Eun S Park

Faculty, Staff and Student Publications

Mutation of KRAS in endothelial cells (KRAS-EC) leads to intracerebral hemorrhage (ICH) in brain arteriovenous malformations (bAVM), resulting in severe disabilities or even death. However, it is unclear what causes this hemorrhagic conversion of bAVM. Here, using a locally established, clinically-relevant sporadic bAVM mouse model, created by overexpressing mutant KRAS (KRASG12V) in the brain EC, we demonstrate that KRAS-EC act as trigger for microglia (MG) activation and infiltration of macrophages (Mϕ). Using three-dimensional immunostaining approach with cleared human and mouse bAVM tissues, we demonstrate an abundance of MG/Mϕ around the bAVM nidus. The presence of MG/Mϕ are correlated to the …

Early Postnatal Polymerase Chain Reaction Testing In The Identification Of Perinatal Transmission Of Hepatitis C Virus, Mona Prasad, Grecio J Sandoval, George R Saade, Brenna L Hughes, Rebecca G Clifton, Uma M Reddy, Anna Bartholomew, Ashley Salazar, Edward K Chien, Alan T N Tita, John M Thorp, Torri D Metz, Ronald J Wapner, Vishakha Sabharwal, Hyagriv N Simhan, Geeta K Swamy, Kent D Heyborne, Baha M Sibai, William A Grobman, Yasser Y El-Sayed, Brian M Casey, Samuel Parry, George A Macones

Faculty, Staff and Student Publications

In this study, a single hepatitis C virus (HCV) RNA at 2-6 months was sensitive and specific (86.7% and 95% confidence interval [CI], 62.1%-96.3% and 100% and 95% CI, 98.8%-100%, respectively) in identifying perinatal transmission of HCV. No cases of perinatal infection requiring treatment were missed.

Epidemiology Of Healthcare-Associated Ventriculitis And Meningitis (Hcavm) And Community-Acquired Meningitis/Encephalitis And Evaluation Of An Off-Label Pcr Panel For Hcavm Diagnosis, Jaime Nassur, Katarina Schnell, Christine Dolon, Laura Walters, Devin Weber, Matthew Pettengill

Department of Medicine Faculty Papers

Healthcare-associated ventriculitis and meningitis (HCAVM) is associated with high morbidity and mortality, but rapid diagnostic tests intended to cover microorganisms that typically cause HCAVM are not commercially available. We sought to evaluate the etiology of HCAVM compared to community-acquired meningitis/encephalitis (CAME) at our healthcare system, and to study the utility of repurposing a multiplex molecular panel intended for positive blood cultures for HCAVM cases. Our epidemiologic review demonstrated that HCAVM cases were primarily caused by bacteria and fungi also associated with bloodstream infections, in contrast with CAME cases, which were primarily caused by herpesviruses and Cryptococcus. Eighty-two cerebrospinal fluid …

Longitudinal Multiomic Signatures Of Ards And Sepsis Inflammatory Phenotypes Identify Pathways Associated With Mortality, Narges Alipanah-Lechner, Pratik Sinha, Et Al.

2020-Current year OA Pubs

BACKGROUNDCritically ill patients with acute respiratory distress syndrome (ARDS) and sepsis exhibit distinct inflammatory phenotypes with divergent clinical outcomes, but the underlying molecular mechanisms remain poorly understood. These phenotypes, derived from clinical data and protein biomarkers, were associated with metabolic differences in a pilot study.METHODSWe performed integrative multiomics analysis of blood samples from 160 patients with ARDS in the ROSE trial, randomly selecting 80 patients from each latent class analysis-defined inflammatory phenotype (hyperinflammatory and hypoinflammatory) with phenotype probability greater than 0.9. Untargeted plasma metabolomics and whole-blood transcriptomics at day 0 and day 2 were analyzed using multimodal factor analysis (MEFISTO). …

Estimated Effectiveness Of 2024-2025 Covid-19 Vaccination Against Severe Covid-19, Kevin C Ma, Jennie H Kwon, Et Al.

2020-Current year OA Pubs

IMPORTANCE: As SARS-CoV-2 JN.1 lineage descendants continue to evolve, evaluating COVID-19 vaccine effectiveness (VE) against severe COVID-19 remains important to guide vaccination strategies.

OBJECTIVE: To estimate the VE of the 2024-2025 COVID-19 vaccines against COVID-19-associated hospitalization and severe in-hospital outcomes overall and by time since dose (7-89, 90-179, and ≥180 days), JN.1 descendant lineage (KP.3.1.1, XEC, LP.8.1), and spike protein mutations associated with immune evasion.

DESIGN, SETTING, AND PARTICIPANTS: This multicenter, test-negative, case-control study conducted by the Investigating Respiratory Viruses in the Acutely Ill Network included adult patients (aged ≥18 years) hospitalized between September 1, 2024, and April 30, 2025, …

Diagnostically Complex Case Of Trivalvular Infectious Endocarditis Complicated By Hiv, Hcv, Pulmonary Septic Emboli, And Epidural Abscess, Madison Baker, Natasha Singh, Rohail A. Baig, Justin Nistico

Advances in Clinical Medical Research and Healthcare Delivery

Background:

Infective endocarditis (IE) can be visualized on echocardiograms. However, there is a significant discrepancy between transthoracic and transesophageal echocardiograms. This imaging modality is also impacted by operator dependent factors. The risk of right sided endocarditis is elevated in people who inject drugs (PWID). In individuals with human immunodeficiency virus (HIV), there is an increased risk of IE, and there is also a relationship that has yet to be fully established between hepatitis C virus (HCV) and IE.

This report describes a woman with a history of IVDU who was diagnosed with HIV/AIDS, HCV, and sepsis secondary to methicillin-resistant Staphylococcus …

A Case Of Fatal Herpes Zoster Ophthalmicus And Encephalitis In An Immunocompetent Host With A Review Of Literature, Kellyn E. Wilkes, Rutwik Pradeep Sharma, Laurie Proia

Advances in Clinical Medical Research and Healthcare Delivery

Herpes zoster is a common disease that can have several complications. Here, we present a case of herpes zoster ophthalmicus with coexisting encephalitis that unfortunately resulted in patient mortality. A 70-year-old male with a past medical history of Parkinson’s disease and schizophrenia presented to the emergency department after being found altered at home. Physical exam was notable for left-sided crusted facial rash, left conjunctival injection, and purulent drainage coming from the right eye. Given the location and appearance of his rash, he was diagnosed with herpes zoster ophthalmicus. There was suspicion for encephalitis given his altered mental status but unfortunately, …

Mycobacterium Shimoidei: A Case Report Of A Rare Nontuberculous Mycobacterial Infection In An American Patient With A Favorable Outcome, Madison Baker, Farah Majdoub, Asad Nasir

Advances in Clinical Medical Research and Healthcare Delivery

Non-tuberculous mycobacteria (NTM) are common environmental pathogens, but they are an uncommon cause of illness. One such mycobacteria, Mycobacterium shimoidei, was discovered in 1968 and found to cause a respiratory illness in 1975. Since then, fewer than 100 cases have been reported worldwide. Symptoms can include cough, fever, weight loss, and hemoptysis This report describes an American patient with no travel history who was found to have significant pulmonary disease caused by this rare non-tuberculous mycobacteria.

Proceeding Book Of The 17th Indonesian Occupational Medicine Updates (Iomu), Perdoki .

Occupational and Environmental Medicine Journal of Indonesia

Bali, Indonesia, 16th - 18th May 2025

Variation In Antiviral Immunity And Inflammation Pathways Precedes Hiv-1 Infection In A High-Risk African Cohort, Mwikali Kioko, Shaban Mwangi, Lynn Fwambah, Amin Hassan, Jason Blackard, Philip Bejon, Eduard Sanders, Thumbi Ndung’U, Eunice Nduati, Abdirahman Abdi

Institute for Human Development, East Africa

BACKGROUND. Susceptibility to HIV-1 infection varies between individuals, but the biological determinants of acquisition risk remain poorly defined.

METHODS. We conducted a case-control study nested within a high-risk cohort in Kenya. We compared the plasma extracellular RNA collected before HIV-1 acquisition with that from matched uninfected individuals acting as controls to identify immunological processes linked to infection risk.

RESULTS. Individuals who later acquired HIV-1 exhibited upregulation of immune processes that facilitate viral infection, including T cell suppression and type II IFN and Th2 immune responses. In contrast, processes associated with antiviral defence and tissue repair, such as …

Patient, Family And Clinician Priorities For Critical Care Research In Asia And Africa: A James Lind Alliance Priority Setting Partnership Using Modified Delphi And Nominal Group Techniques, Ccaa Priority Setting Partnership Steering Group, Teddy Abonyo, Sumaiya Arfin, Diptesh Aryal, Abi Beane, Martina Borellini, Arjen Dondorp, Emma Donley, Punam Gautam, Tiffany Gooden

Anaesthesiology, East Africa

Background This James Lind Alliance (JLA) Priority Setting Partnership aimed to identify and prioritise unanswered questions important to adult patients, their families and health professionals with lived experience of critical care across Asia and Africa.

Methods Modified Delphi techniques were used to generate suggestions using an online survey. Following verification, literature review and content analysis, these suggestions were iteratively codified into emergent topics. Topics were presented in a second online survey for ranking, prior to an online workshop where nominal group technique was used to identify top priority questions across stakeholder groups. Surveys were disseminated using snowballing techniques.

Findings The …

Nasal Microbiome And Phageome Profiles Are Associated With Prospective Respiratory Viral Infection Risk In School-Age Children, Michael S Kelly, Ching-Ying Huang, Minsik Kim, Dastan Haghnazari, Aribah Baig, Ye Sun, Bryan R Lenneman, Michael J Tisza, Amparito Cunningham, Diane Gold, Wanda Phipatanakul, Peggy S Lai

Faculty, Staff and Students Publications

Background: Respiratory viral infections are common and can trigger asthma exacerbations in children. The roles of the nasal microbiome and phageome (viruses that infect microbes) are not well understood.

Objective: We sought to characterize the epidemiology of respiratory viral infections and the interplay between the nasal microbiome, phageome, and viral infections in school-age children with asthma.

Methods: We performed metagenomic sequencing and quantitative RT-PCR detection of respiratory viruses on 375 nasal samples from 227 school-age children with asthma collected routinely 3 times over a year. Surveys on parent-reported cold and asthma symptoms were administered routinely every 2 months. We evaluated …

Epidemiology And Outcomes Of Sporotrichosis: A Descriptive Real-World Analysis From A Global Cohort, Samantha Schapiro, Nicholas Pulciano, Julian Galindo-Ramirez, Nicholas Rau, Jose Tuells, Nelson Iván Agudelo Higuita, George R. Thompson Iii, Daniel B. Chastain, Andrés F. Henao-Martínez

School of Medicine Publications

Background: Sporotrichosis is a dimorphic fungal infection of increasing global relevance. Although usually cutaneous or lymphocutaneous, disseminated disease occurs in immunocompromised hosts. Large-scale data on its epidemiology, treatment and outcomes remain limited.

Objectives: To characterise the clinical features, comorbidities, antifungal prescribing patterns and one-year mortality associated with sporotrichosis, with emphasis on patients with HIV and other forms of immunosuppression.

Patients/methods: We performed a retrospective global cohort study using the TriNetX Research Network. Adults (≥ 18 years) diagnosed with sporotrichosis were identified using ICD-9/10 codes (1995-2024). Demographics, comorbidities, laboratory parameters and antifungal prescriptions were analysed. The primary outcome was all-cause mortality …

The Global Cancer Crisis: A Review Of Growing Burden, Deepening Inequality And Initiatives For Prevention And Early Detection, Charles Yankah, Jonathan Nwiloh, Carlos Mestres, Abdelmalek Bouzid, Tom Mwambu, Andrew Duncan, Mohamed Debieche, Samuel Omokhodion, Uvie Onakpoya, Matthias Angres

General Surgery, East Africa

Cancer constitutes one of the most urgent global health crises, with over 20 million new cases diagnosed annually worldwide, claiming 10 million lives. This devastating burden disproportionately affects vulnerable populations: 75% of cancer deaths occur in low- and middle-income countries despite these regions having lower reported incidence rates. Lung cancer leads the global toll, representing 12% of all cases but 19% of deaths, followed by breast cancer (12% of cases) and colorectal cancer (9.6%). A stark geographical inequity defines the cancer landscape—while wealthy regions such as North America, Northern Europe and Australia report the highest incidence rates, Africa and Latin …

Integration Of One Health Activities Into Professional Student Education: Successes, Challenges, And Considerations, Karen Gruszynski, Mary Beth Babos, Reagan Bishop, Debra Sullivan, Laroy Brandt

All Faculty and Staff Scholarship

Interprofessional Education (IPE) creates opportunities for multiple disciplines to learn from each other and develop soft skills to improve patient care. One Health similarly emphasizes collaborative and interdisciplinary practice while recognizing the interconnectedness between human, animal, and environmental health. Despite the intersection of IPE and One Health, the meaningful integration of One Health within IPE remains uneven and difficult to operationalize. This perspective synthesizes experiences from multi-college programs implementing One Health-oriented IPE, highlighting successes, challenges, and structural requirements. We argue that for One Health to be successfully integrated into IPE for professional students, it requires extensive logistical planning, coordinated institutional …

Controlled Antibiotic Release From Emulsion-Loaded Alginate And Fibrin Hydrogels Using Ultrasound, Ziba Ghareh Nazi Fam, Asia Winslow, Mario Fabiilli, Sam Varghese, Brian Oeffinger, Flemming Forsberg, Noreen Hickok, Lauren Delaney

Department of Radiology Faculty Papers

Postoperative infections remain a major complication after spinal fusion surgery, often caused by biofilm-forming bacteria that resist short-term antibiotic prophylaxis. Vancomycin (VAN) is sometimes delivered locally during surgery; however, levels diminish rapidly, leaving patients vulnerable to late-onset infections. We developed a composite hydrogel integrating perfluorohexane-based emulsions within alginate or fibrin matrices to enable both sustained and ultrasound-triggered VAN release. Water-in-oil-in-water emulsions were prepared using fluorosurfactant-stabilized perfluorohexane as the volatile oil phase, then embedded in hydrogels and exposed to ultrasound (2.5 MHz, 5.5 MPa peak negative pressure) to initiate acoustic droplet vaporization for triggered release. Drug release was quantified spectrophotometrically and …

Investigation Of Teratogenic Concerns In The Coronavirus Disease Of 2019 Era, Kate Richardson, Emily C Daykin, Kathleen Shields, S Shahrukh Hashmi, Lorrie Harris-Sagaribay, Molly Daniels, Myla Ashfaq

Faculty, Staff and Student Publications

Background: MotherToBaby (MTB) is a teratogen information service that provides information about exposures during pregnancy and breastfeeding to the public and healthcare providers. During the Coronavirus Disease of 2019 (COVID-19) pandemic, MTB received an influx of queries regarding the teratogenicity of the virus and the vaccine. The purpose of this study was to assess the frequency and type of exposures asked about prior to the onset of the COVID-19 pandemic through March 2022 and to evaluate the demographics of individuals who made inquiries.

Methods: Data from MTB contacts (2018-2022) were accessed through a data-sharing agreement. The data were cleaned and …

From A Papule To Friable Papillary Projections: A Case Of Old World Cutaneous Leishmaniasis, Zamanali Khakhar, Adil Salyani, Soraiya Manji, Rajiv Patel, Sayed Karar

Internal Medicine, East Africa

This case aims to characterize an unusual cutaneous manifestation in a patient with confirmed cutaneous leishmaniasis, highlighting clinical features that are often underrecognized and may contribute to diagnostic uncertainty. By exploring this atypical presentation, it underscores the potential for misdiagnosis and its implications for patient management. Additionally, it emphasizes the broad spectrum of cutaneous lesions that can mimic Old World cutaneous leishmaniasis, further increasing the risk of diagnostic error.

Development Of A Predictive Model For Cardiac Dysfunction In Mis-C Patients Utilizing Laboratory Biomarkers, Guliz Erdem, Brendan Galdo, Roshini S Abraham, Allayne Stephans, Simon Lee, Jun Yasuhara, Brent Merryman, Diego Cruz Vidal, Nathan M Money, Jennifer Colgan, Risa Bochner, Ron L Kaplan, Erin Aldag, Thomas Graf, Steve Rust

Faculty, Staff and Student Publications

Background and objectives: Early identification of cardiac dysfunction in multi-system inflammatory syndrome in children (MIS-C) is crucial for effective management. Our primary objective was to predict left ventricular systolic dysfunction (LVSD) through a multicenter collaborative assessing admission laboratory data and echocardiogram findings.

Methods: Laboratory and clinical data were collected by retrospective chart review from a cohort of pediatric patients admitted and treated for MIS-C in our institutions. Laboratory data including absolute lymphocyte count, albumin, sedimentation rate, C-reactive protein, procalcitonin, d-dimer, fibrinogen, ferritin, interleukin-6 level, and lymphocyte subsets (T, B and NK quantitation, TBNK) were collected. We built a LASSO logistic …

Kawasaki Disease, Children's Mercy Kansas City

Clinical Pathways

No abstract provided.

Acute Otitis Media: Antibiotic Length, Children's Mercy Kansas City

Clinical Critically Appraised Topics

No abstract provided.

“Now That The Baby Is Out, I Can Be Vaccinated”: A Qualitative Study On Covid-19 Vaccine Hesitancy In Pregnant Women In Kilifi, Kenya, Angela Koech, Onesmus Wanje, Grace Mwashigadi, Geoffrey Katana, Richmond Mdindi, Peter Mwangome, Rachel Craik, Marianne Vidler, Mai-Lei Kinshella, Marleen Temmerman

Centre of Excellence in Women and Child Health

COVID-19 vaccines are safe and effective in pregnancy, but vaccine hesitancy limits uptake and effectiveness. This study explored COVID-19 vaccine hesitancy in pregnancy in Kilifi, coastal Kenya, to elicit reasons for vaccine hesitancy and acceptance, and to compile misconceptions around vaccination in pregnancy. Twenty-three in-depth interviews were conducted with pregnant women, mothers who had given birth in the previous 2 years and health workers (community health promoters, nurses, and supervisors). Data were analyzed using thematic template analysis based on the Vaccine Hesitancy Determinants Matrix. Concern about vaccine safety for the unborn baby was a major driver of hesitancy. Many pregnant …

Diagnostic Evaluation And Treatment Of Utis In Children With Neurogenic Bladder, Jacqueline G Holden, Sowdhamini Wallace, Pearl W Chang, Stephanie Davis-Rodriguez, Rana F Hamdy, John M Morrison, Michael J Tchou, Victor Trevisanut, Vijaya Vemulakonda, Catherine S Forster

Faculty, Staff and Students Publications

Objective: Children with neurogenic bladder (NGB) are at increased risk for urinary tract infections (UTIs), but there is a lack of guidelines to assist clinicians in diagnosing and treating these children. Our objective was to describe the presentation and treatment of provider diagnosed UTIs in children with NGB compared to children with vesicoureteral reflux (VUR) and to assess the proportion of children with NGB who met a consortium definition of UTI.

Study design: We included children < 18 years old with either VUR or NGB who were diagnosed in the emergency department with a febrile UTI in our multicenter retrospective cohort study. We extracted and compared UTI symptoms and urinalysis results specific to children with NGB to children with VUR. We measured the proportion of UTI diagnoses concordant with the Urologic Management to Preserve Initial Renal Function (UMPIRE) consensus definition of UTI, defined as ≥ 100,000 CFU/mL of 1 or 2 organisms, pyuria, and ≥ two symptoms of UTI.

Results: The most common symptom among all children in the cohort was vomiting (38.8 %). Of the 215 children with NGB, 41.3 % met …

A Scalable Organoid Model Of Urothelial Aging For Metabolic Interrogation, Infection Modeling, And Reversal Of Age-Associated Changes, Adwaita R Parab, Arnold M Salazar, Steven J Bark, Margarita Divenko, Vasanta Putluri, D'Feau J Lieu, Aadya S Singh, Nagireddy Putluri, Indira U Mysorekar

Faculty, Staff and Students Publications

Aging leads to a progressive decline in overall bladder function resulting in lower urinary tract symptoms and increased susceptibility to infections. However, tissue-specific mechanisms of aging, specifically the contributions of the urothelium, remain elusive. Here, we introduce mouse bladder epithelium-derived organoids (mBEDOs) as a scalable platform to model urothelial aging. mBEDOs from aged mice recapitulate key features of age-associated cellular reprogramming, including oxidative stress, senescence, and DNA damage. We demonstrate the utility of mBEDOs for modeling Uropathogenic Escherichia coli (UPEC) infection, generating assembloids between mBEDOs and macrophages to model epithelial-immune interactions, and genetic perturbation. Using the mBEDO platform, we also …

Cressent: A Bioinformatics Toolkit To Explore And Improve Ssdna Virus Annotation, Ricardo R Pavan, Matthew B Sullivan, Michael J Tisza

Faculty, Staff and Students Publications

ssDNA viruses are important components of diverse ecosystems; however, it remains challenging to systematically identify and classify them. This is partly due to their broad host range and resulting genomic diversity, structure and rapid evolutionary rates. In addition, distinguishing genuine ssDNA genomes from contaminating sequences in metagenomic datasets (e.g. from commercial kits) has been an unresolved issue for years. Here, we present CRESSENT (CRESS-DNA Extended aNnotation Toolkit), a comprehensive and modular bioinformatic pipeline focused on ssDNA virus 'genome-to-analysis' and annotation. The pipeline integrates multiple functionalities organized into several modules: sequence dereplication, decontamination, phylogenetic analysis, …