Digital Commons Network^™

A Deep Learning Convolutional Neural Network Can Differentiate Between Helicobacter Pylori Gastritis And Autoimmune Gastritis With Results Comparable To Gastrointestinal Pathologists, Michael M. Franklin, Fred A. Schultz, Marissa A. Tafoya, Audra A. Kerwin, Cory J. Broehm, Edgar G. Fischer, Rama R. Gullapalli, Douglas P. Clark, Joshua A. Hanson, David R. Martin

Pathology Research and Scholarship

CONTEXT.—: Pathology studies using convolutional neural networks (CNNs) have focused on neoplasms, while studies in inflammatory pathology are rare. We previously demonstrated a CNN that differentiates reactive gastropathy, Helicobacter pylori gastritis (HPG), and normal gastric mucosa.

OBJECTIVE.—: To determine whether a CNN can differentiate the following 2 gastric inflammatory patterns: autoimmune gastritis (AG) and HPG.

DESIGN.—: Gold standard diagnoses were blindly established by 2 gastrointestinal (GI) pathologists. One hundred eighty-seven cases were scanned for analysis by HALO-AI. All levels and tissue fragments per slide were included for analysis. The cases were randomized, 112 (60%; 60 HPG, 52 AG) in the …

Reduced Cleavage Of Von Willebrand Factor By Adamts13 Is Associated With Microangiopathic Acute Kidney Injury Following Trauma, William E. Plautz, Shannon H. Haldeman, Mitchell R. Dyer, Jason L. Sperry, Francis X. Guyette, Patricia A. Loughran, Jurgis Alvikas, Adnan Hassoune, Lara Hoteit, Nijmeh Alsaadi, Brian S. Zuckerbraun, Marian A. Rollins-Raval, Jay S. Raval, Roberto I. Mota, Matthew D. Neal

Pathology Research and Scholarship

Acute kidney injury (AKI) is common after trauma, but contributory factors are incompletely understood. Increases in plasma von Willebrand Factor (vWF) with concurrent decreases in ADAMTS13 are associated with renal microvascular thrombosis in other disease states, but similar findings have not been shown in trauma. We hypothesized that molecular changes in circulating vWF and ADAMTS13 promote AKI following traumatic injury. VWF antigen, vWF multimer composition and ADAMTS13 levels were compared in plasma samples from 16 trauma patients with and without trauma-induced AKI, obtained from the Prehospital Air Medical Plasma (PAMPer) biorepository. Renal histopathology and function, vWF and ADAMTS13 levels were …

Higher Amyloid Is Associated With Greater Loneliness Among Cognitively Normal Older Adults During The Covid-19 Pandemic [Version 2; Peer Review: 2 Approved], Abigail Kehrer-Dunlap, Rebecca Bollinger, Szu-Wei Chen, Audrey Keleman, Regina Thompson, Anne Fagan, Beau Ances, Susan Stark

2020-Current year OA Pubs

BACKGROUND: Loneliness has been associated with several consequences, including increased risk of developing Alzheimer disease (AD). Loneliness may arise during the preclinical phase of AD, but little is known about the relationship between loneliness and amyloid accumulation consistent with preclinical AD. Therefore, the purpose of this study was to examine the relationship between amyloid accumulation and subjective experiences of loneliness among cognitively normal older adults during the COVID-19 pandemic.

METHODS: A global Clinical Dementia Rating

RESULTS: The 108 participants had a mean age of 75.0 and an average amyloid accumulation of 22.2 ± 31.9. Mean UCLA Loneliness Scale scores were …

What Does It Mean To Be Affiliated With Care?: Delphi Consensus On The Definition Of "Unaffiliation" And "Specialist" In Sickle Cell Disease, Andrea E. Lamont, Lewis L. Hsu, Sara Jacobs, Robert Gibson, Marsha Treadwell, Yumei Chen, Richard Lottenberg, Kathleen Axelrod, Taniya Varughese, Cathy Melvin, Sharon Smith, Ifeanyi Beverly Chukwudozie, Julie Kanter, Sickle Cell Disease Implementation Consortium

2020-Current year OA Pubs

Accruing evidence reveals best practices for how to help individuals living with Sickle Cell Disease (SCD); yet, the implementation of these evidence-based practices in healthcare settings is lacking. The Sickle Cell Disease Implementation Consortium (SCDIC) is a national consortium that uses implementation science to identify and address barriers to care in SCD. The SCDIC seeks to understand how and why patients become unaffiliated from care and determine strategies to identify and connect patients to care. A challenge, however, is the lack of agreed-upon definition for what it means to be unaffiliated and what it means to be a "SCD expert …

Barriers And Facilitators To Diabetes Screening And Prevention After A Pregnancy Complicated By Gestational Diabetes, Drishti D. Sinha, Roxann C. Williams, Laura N. Hollar, Hannah R. Lucas, Bethany Johnson-Javois, Heidi B. Miller, Amanda Stoermer, Graham A. Colditz, Aimee S. James, Cynthia J. Herrick

2020-Current year OA Pubs

OBJECTIVE: Gestational diabetes mellitus (GDM) is increasing in the United States, with higher rates among minoritized racial and ethnic populations and lower income populations. GDM increases risk for type 2 diabetes (T2DM), and postpartum diabetes screening and prevention are imperative. This qualitative study examines barriers and facilitators to postpartum T2DM screening and prevention among non-privately insured individuals with a history of GDM in a state prior to Medicaid expansion.

METHODS: Thirty-six non-privately insured women with a history of GDM completed semi-structured interviews. Four focus groups and seven interviews were conducted with 30 nurse practitioners, physicians, physician assistants, nurses and registered …

Mitochondrial Fitness And Cancer Risk, Andrew V. Kossenkov, Andrew Milcarek, Faiyaz Notta, Gun-Ho Jang, Julie M. Wilson, Steven Gallinger, Daniel Cui Zhou, Li Ding, Jagadish C. Ghosh, Michela Perego, Annamaria Morotti, Marco Locatelli, Marie E. Robert, Valentina Vaira, Dario C. Altieri

2020-Current year OA Pubs

Changes in metabolism are a hallmark of cancer, but molecular signatures of altered bioenergetics to aid in clinical decision-making do not currently exist. We recently identified a group of human tumors with constitutively reduced expression of the mitochondrial structural protein, Mic60, also called mitofilin or inner membrane mitochondrial protein (IMMT). These Mic60-low tumors exhibit severe loss of mitochondrial fitness, paradoxically accompanied by increased metastatic propensity and upregulation of a unique transcriptome of Interferon (IFN) signaling and Senescence-Associated Secretory Phenotype (SASP). Here, we show that an optimized, 11-gene signature of Mic60-low tumors is differentially expressed in multiple malignancies, compared to normal …

Inclusion Of Children With Disabilities In Qualitative Health Research: A Scoping Review, Janet Njelesani, Vongai Mlambo, Tsedenia Denekew, Jean Hunleth

2020-Current year OA Pubs

BACKGROUND: Children with disabilities have the right to participate in health research so their priorities, needs, and experiences are included. Health research based primarily on adult report risks misrepresenting children with disabilities and their needs, and contributes to exclusion and a lack of diversity in the experiences being captured. Prioritizing the participation of children with disabilities enhances the relevance, meaningfulness, and impact of research.

METHODS: A scoping review was conducted to critically examine the participation of children with disabilities in qualitative health research. The electronic databases PubMed, PsychInfo, Embase, and Google Scholar were searched. Inclusion criteria included qualitative health studies …

Neonatal Motor Functional Connectivity And Motor Outcomes At Age Two Years In Very Preterm Children With And Without High-Grade Brain Injury, Peppar E P Cyr, Rachel E Lean, Jeanette K Kenley, Sydney Kaplan, Dominique E Meyer, Jeffery J Neil, Dimitrios Alexopoulos, Rebecca G Brady, Joshua S Shimony, Thomas L Rodebaugh, Cynthia E Rogers, Christopher D Smyser

2020-Current year OA Pubs

Preterm-born children have high rates of motor impairments, but mechanisms for early identification remain limited. We hypothesized that neonatal motor system functional connectivity (FC) would relate to motor outcomes at age two years; currently, this relationship is not yet well-described in very preterm (VPT; born <32 weeks' gestation) infants with and without brain injury. We recruited 107 VPT infants - including 55 with brain injury (grade III-IV intraventricular hemorrhage, cystic periventricular leukomalacia, post-hemorrhagic hydrocephalus) - and collected FC data at/near term-equivalent age (35-45 weeks postmenstrual age). Correlation coefficients were used to calculate the FC between bilateral motor and visual cortices and thalami. At two years corrected-age, motor outcomes were assessed with the Bayley Scales of Infant and Toddler Development, 3rd edition. Multiple imputation was used to estimate missing data, and regression models related FC measures to motor outcomes. Within the brain-injured group only, interhemispheric motor cortex FC was positively related to gross motor outcomes. Thalamocortical and visual FC were not related to motor scores. This suggests neonatal alterations in motor system FC may provide prognostic information about impairments in children with brain injury.

The First 20 Months Of The Covid-19 Pandemic: Mortality, Intubation And Icu Rates Among 104,590 Patients Hospitalized At 21 United States Health Systems, Michael C. Fiore, Li-Shiun Chen, Et Al.

2020-Current year OA Pubs

MAIN OBJECTIVE: There is limited information on how patient outcomes have changed during the COVID-19 pandemic. This study characterizes changes in mortality, intubation, and ICU admission rates during the first 20 months of the pandemic.

STUDY DESIGN AND METHODS: University of Wisconsin researchers collected and harmonized electronic health record data from 1.1 million COVID-19 patients across 21 United States health systems from February 2020 through September 2021. The analysis comprised data from 104,590 adult hospitalized COVID-19 patients. Inclusion criteria for the analysis were: (1) age 18 years or older; (2) COVID-19 ICD-10 diagnosis during hospitalization and/or a positive COVID-19 PCR …

Protocol For The Ketamine For Postoperative Avoidance Of Depressive Symptoms (K-Pass) Feasibility Study: A Randomized Clinical Trial, Bradley A Fritz, Bethany R Tellor Pennington, Ben J A Palanca, Julie A Schweiger, Jon T Willie, Nuri B Farber

2020-Current year OA Pubs

No abstract provided.

Sars-Cov-2 Booster Vaccination Rescues Attenuated Igg1 Memory B Cell Response In Primary Antibody Deficiency Patients, Frank J Lin, Alexa Michelle Altman Doss, Hannah G Davis-Adams, Lucas J Adams, Christopher H Hanson, Laura A Vanblargan, Chieh-Yu Liang, Rita E Chen, Jennifer Marie Monroy, H James Wedner, Anthony Kulczycki, Tarisa L Mantia, Caitlin C O'Shaughnessy, Saravanan Raju, Fang R Zhao, Elise Rizzi, Christopher J Rigell, Tiffany Biason Dy, Andrew L Kau, Zhen Ren, Jackson S Turner, Jane A O'Halloran, Rachel M Presti, Daved H Fremont, Peggy L Kendall, Ali H Ellebedy, Philip A Mudd, Michael S Diamond, Ofer Zimmerman, Brian J Laidlaw

2020-Current year OA Pubs

BACKGROUND: Although SARS-CoV-2 vaccines have proven effective in eliciting a protective immune response in healthy individuals, their ability to induce a durable immune response in immunocompromised individuals remains poorly understood. Primary antibody deficiency (PAD) syndromes are among the most common primary immunodeficiency disorders in adults and are characterized by hypogammaglobulinemia and impaired ability to mount robust antibody responses following infection or vaccination.

METHODS: Here, we present an analysis of both the B and T cell response in a prospective cohort of 30 individuals with PAD up to 150 days following initial COVID-19 vaccination and 150 days post mRNA booster vaccination. …

Temporal Cohort Logic, Guo-Qiang Zhang, Xiaojin Li, Yan Huang, Licong Cui

Faculty, Staff and Student Publications

We introduce a new logic, called Temporal Cohort Logic (TCL), for cohort specification and discovery in clinical and population health research. TCL is created to fill a conceptual gap in formalizing temporal reasoning in biomedicine, in a similar role that temporal logics play for computer science and its applications. We provide formal syntax and semantics for TCL and illustrate the various logical constructs using examples related to human health. Relationships and distinctions with existing temporal logical frameworks are discussed. Applications in electronic health record (EHR) and in neurophysiological data resource are provided. Our approach differs from existing temporal logics, in …

Automated Identification Of Missing Is-A Relations In The Human Phenotype Ontology, Maryamsadat Mohtashamian, Ran Hu, Rashmie Abeysinghe, Xubing Hao, Hua Xu, Licong Cui

Faculty, Staff and Student Publications

Auditing the Human Phenotype Ontology (HPO) is necessary to provide accurate terminology for its use in clinical research. We investigate an approach leveraging the lexical features of concepts in HPO to identify missing IS-A relations among HPO concepts. We first model the names of HPO concepts as sets of words in lower case. Then, we generate two types of concept-pairs which have at least a single common word: (1) Linked concept-pairs generated from concept-pairs having an IS-A relation; (2) Unlinked concept-pairs generated from concept-pairs without an IS- A relation. Concept-pairs generate Derived Term Pairs (DTPs) emphasizing unique lexical information of …

Cost Of Care For Asylum Seekers And Refugees Entering The United States: The Case Of Volunteer Medical Providers In El Paso, Texas, Rigoberto I Delgado, Manuel De La Rosa, Marlon A Picado, Lisa Ayoub-Rodriguez, Celia E Gonzalez, Leopold Gemoets

Faculty, Staff and Student Publications

BACKGROUND: Between October 2018, and February 2020, the United States saw an unprecedented increase in the number of asylum seekers and refugees arriving unexpectedly at international crossings along the US-Mexico Border. Many of these migrants needed proper medical attention, and consequently created significant pressure on local health systems. In El Paso, Texas, volunteer clinicians, collaborating closely with religious organizations and non-governmental organizations, provided outpatient medical care for the new arrivals; the county hospital provided in-patient care at local tax payers' expense. The objective of this study was to estimate costs of healthcare services offered by these volunteers in order to …

Racial And Socioeconomic Disparities In Patients With Meningioma: A Retrospective Cohort Study, Hudin N Jackson, Caroline C Hadley, A Basit Khan, Ron Gadot, James C Bayley, Arya Shetty, Jacob Mandel, Ali Jalali, K Kelly Gallagher, Alex D Sweeney, Arif O Harmanci, Akdes S Harmanci, Tiemo Klisch, Shankar P Gopinath, Ganesh Rao, Daniel Yoshor, Akash J Patel

Faculty, Staff and Student Publications

BACKGROUND: Meningiomas are the most common intracranial neoplasms. Although genomic analysis has helped elucidate differences in survival, there is evidence that racial disparities may influence outcomes. African Americans have a higher incidence of meningiomas and poorer survival outcomes. The etiology of these disparities remains unclear, but may include a combination of pathophysiology and other factors.

OBJECTIVE: To determine factors that contribute to different clinical outcomes in racial populations.

METHODS: We retrospectively reviewed 305 patients who underwent resection for meningiomas at a single tertiary care facility. We used descriptive statistics and univariate, multivariable, and Kaplan-Meier analyses to study clinical, radiographical, and …

Risk Of Alzheimer's Disease Following Influenza Vaccination: A Claims-Based Cohort Study Using Propensity Score Matching, Avram S Bukhbinder, Yaobin Ling, Omar Hasan, Xiaoqian Jiang, Yejin Kim, Kamal N Phelps, Rosemarie E Schmandt, Albert Amran, Ryan Coburn, Srivathsan Ramesh, Qian Xiao, Paul E Schulz

Faculty, Staff and Student Publications

BACKGROUND: Prior studies have found a reduced risk of dementia of any etiology following influenza vaccination in selected populations, including veterans and patients with serious chronic health conditions. However, the effect of influenza vaccination on Alzheimer's disease (AD) risk in a general cohort of older US adults has not been characterized.

OBJECTIVE: To compare the risk of incident AD between patients with and without prior influenza vaccination in a large US claims database.

METHODS: Deidentified claims data spanning September 1, 2009 through August 31, 2019 were used. Eligible patients were free of dementia during the 6-year look-back period and≥65 years …

Fairly Predicting Graft Failure In Liver Transplant For Organ Assigning, Sirui Ding, Ruixiang Tang, Daochen Zha, Na Zou, Kai Zhang, Xiaoqian Jiang, Xia Hu

Faculty, Staff and Student Publications

Liver transplant is an essential therapy performed for severe liver diseases. The fact of scarce liver resources makes the organ assigning crucial. Model for End-stage Liver Disease (MELD) score is a widely adopted criterion when making organ distribution decisions. However, it ignores post-transplant outcomes and organ/donor features. These limitations motivate the emergence of machine learning (ML) models. Unfortunately, ML models could be unfair and trigger bias against certain groups of people. To tackle this problem, this work proposes a fair machine learning framework targeting graft failure prediction in liver transplant. Specifically, knowledge distillation is employed to handle dense and sparse …

Facilitating Federated Genomic Data Analysis By Identifying Record Correlations While Ensuring Privacy, Leonard Dervishi, Xinyue Wang, Wentao Li, Anisa Halimi, Jaideep Vaidya, Xiaoqian Jiang, Erman Ayday

Faculty, Staff and Student Publications

With the reduction of sequencing costs and the pervasiveness of computing devices, genomic data collection is continually growing. However, data collection is highly fragmented and the data is still siloed across different repositories. Analyzing all of this data would be transformative for genomics research. However, the data is sensitive, and therefore cannot be easily centralized. Furthermore, there may be correlations in the data, which if not detected, can impact the analysis. In this paper, we take the first step towards identifying correlated records across multiple data repositories in a privacy-preserving manner. The proposed framework, based on random shuffling, synthetic record …

Caries Risk Documentation And Prevention: Emeasures For Dental Electronic Health Records, Suhasini Bangar, Ana Neumann, Joel M White, Alfa Yansane, Todd R Johnson, Gregory W Olson, Shwetha V Kumar, Krishna K Kookal, Aram Kim, Enihomo Obadan-Udoh, Elizabeth Mertz, Kristen Simmons, Joanna Mullins, Ryan Brandon, Muhammad F Walji, Elsbeth Kalenderian

Faculty, Staff and Student Publications

BACKGROUND: Longitudinal patient level data available in the electronic health record (EHR) allows for the development, implementation, and validations of dental quality measures (eMeasures).

OBJECTIVE: We report the feasibility and validity of implementing two eMeasures. The eMeasures determined the proportion of patients receiving a caries risk assessment (eCRA) and corresponding appropriate risk-based preventative treatments for patients at elevated risk of caries (appropriateness of care [eAoC]) in two academic institutions and one accountable care organization, in the 2019 reporting year.

METHODS: Both eMeasures define the numerator and denominator beginning at the patient level, populations' specifications, and validated the automated queries. For …

Enhancing Diagnosis Through Technology: Decision Support, Artificial Intelligence, And Beyond, Robert El-Kareh, Dean F Sittig

Faculty, Staff and Student Publications

Patient care in intensive care environments is complex, time-sensitive, and data-rich, factors that make these settings particularly well-suited to clinical decision support (CDS). A wide range of CDS interventions have been used in intensive care unit environments. The field needs well-designed studies to identify the most effective CDS approaches. Evolving artificial intelligence and machine learning models may reduce information-overload and enable teams to take better advantage of the large volume of patient data available to them. It is vital to effectively integrate new CDS into clinical workflows and to align closely with the cognitive processes of frontline clinicians.

A Novel Group Of Genes That Cause Endocrine Resistance In Breast Cancer Identified By Dynamic Gene Expression Analysis, Arvand Asghari, Katherine Wall, Michael Gill, Natascha Del Vecchio, Farnaz Allahbakhsh, Jacky Wu, Nan Deng, W Jim Zheng, Hulin Wu, Michihisa Umetani, Vahed Maroufy

Faculty, Staff and Student Publications

Breast cancer (BC) is the most common type of cancer diagnosed in women. Among female cancer deaths, BC is the second leading cause of death worldwide. For estrogen receptor-positive (ER-positive) breast cancers, endocrine therapy is an effective therapeutic approach. However, in many cases, an ER-positive tumor becomes unresponsive to endocrine therapy, and tumor regrowth occurs after treatment. While some genetic mutations contribute to resistance in some patients, the underlying causes of resistance to endocrine therapy are mostly undetermined. In this study, we utilized a recently developed statistical approach to investigate the dynamic behavior of gene expression during the development of …

Prediction Of Fluid Intelligence From T1-W Mri Images: A Precise Two-Step Deep Learning Framework, Mingliang Li, Mingfeng Jiang, Guangming Zhang, Yujun Liu, Xiaobo Zhou

Faculty, Staff and Student Publications

The Adolescent Brain Cognitive Development (ABCD) Neurocognitive Prediction Challenge (ABCD-NP-Challenge) is a community-driven competition that challenges competitors to develop algorithms to predict fluid intelligence scores from T1-w MRI images. In this work, a two-step deep learning pipeline is proposed to improve the prediction accuracy of fluid intelligence scores. In terms of the first step, the main contributions of this study include the following: (1) the concepts of the residual network (ResNet) and the squeeze-and-excitation network (SENet) are utilized to improve the original 3D U-Net; (2) in the segmentation process, the pixels in symmetrical brain regions are assigned the same label; …

Stigma Towards Mental Illness And Help-Seeking Behaviors Among Adult And Child Psychiatrists In Hungary: A Cross-Sectional Study, Dorottya Őri, Péter Szocsics, Tamás Molnár, Fanni Virág Ralovich, Zsolt Huszár, Ágnes Bene, Sándor Rózsa, Zsuzsa Győrffy, György Purebl

2020-Current year OA Pubs

OBJECTIVE: Stigma towards people with mental health problems is a growing issue across the world, to which healthcare providers might contribute. The aim of the present study was to explore psychiatrists' attitudes towards their patients and link them to psychosocial and professional factors.

METHODS: An online questionnaire was used to approach the in- and outpatient psychiatric services across Hungary. A total of 211 trainees and specialists in adult and child psychiatry participated in our study. Their overall stigmatizing attitudes were measured, with focus on attitude, disclosure and help-seeking, and social distance dimensions by using the self-report Opening Minds Stigma Scale …

Effect Of Acute Postsurgical Pain Trajectories On 30-Day And 1-Year Pain, Saria S Awadalla, Victoria Winslow, Michael S. Avidan, Simon Haroutounian, Thomas G. Kannampallil

2020-Current year OA Pubs

Untreated pain after surgery leads to poor patient satisfaction, longer hospital length of stay, lower health-related quality of life, and non-compliance with rehabilitation regimens. The aim of this study is to characterize the structure of acute pain trajectories during the postsurgical hospitalization period and quantify their association with pain at 30-days and 1-year after surgery. This cohort study included 2106 adult (≥18 years) surgical patients who consented to participate in the SATISFY-SOS registry (February 1, 2015 to September 30, 2017). Patients were excluded if they did not undergo invasive surgeries, were classified as outpatients, failed to complete follow up assessments …

Voting Behavior During Fda Medical Device Advisory Committee Panel Meetings, Amanda Maisel-Campbell, Daniel I Schlessinger, Arianna F. Yanes, Emir Veledar, Kelly A. Reynolds, Sarah A. Ibrahim, Bianca Y. Kang, Noor Anvery, Emily Poon, Murad Alam

2020-Current year OA Pubs

OBJECTIVES: During premarket review, the US Food and Drug Administration may ask its Medical Device Advisory Committee (MDAC) Panels to assess the safety and effectiveness of medical devices being considered for approval. The objective of this study is to assess the relationship, if any, between individual votes and Panel recommendations and: (1) the composition of Panels, specifically the expertise and demographic features of individual members; or (2) Panel members' propensity to speak during Panel deliberations.

METHODS: This was a retrospective cohort study of routinely collected data from voting members of MDAC panels convened between January 2011 to June 2016 to …

Combining Empirical Knowledge, In Silico Molecular Docking And Admet Profiling To Identify Therapeutic Phytochemicals From Brucea Antidysentrica For Acute Myeloid Leukemia, Lemessa Etana Bultum, Gemechu Bekele Tolossa, Doheon Lee

2020-Current year OA Pubs

Acute myeloid leukemia (AML) is one of the deadly cancers. Chemotherapy is the first-line treatment and the only curative intervention is stem cell transplantation which are intolerable for aged and comorbid patients. Therefore, finding complementary treatment is still an active research area. For this, empirical knowledge driven search for therapeutic agents have been carried out by long and arduous wet lab processes. Nonetheless, currently there is an accumulated bioinformatics data about natural products that enabled the use of efficient and cost effective in silico methods to find drug candidates. In this work, therefore, we set out to computationally investigate the …

Checkpoint Blockade-Induced Cd8+ T Cell Differentiation In Head And Neck Cancer Responders, Liye Zhou, Paul Zolkind, Obi Griffith, Et Al

2020-Current year OA Pubs

BACKGROUND: Immune checkpoint blockade (ICB) response in recurrent/metastatic head and neck squamous cell carcinoma (HNSCC) is limited to 15%-20% of patients and underpinnings of resistance remain undefined.

METHODS: Starting with an anti-PD1 sensitive murine HNSCC cell line, we generated an isogenic anti-PD1 resistant model. Mass cytometry was used to delineate tumor microenvironments of both sensitive parental murine oral carcinoma (MOC1) and resistant MOC1esc1 tumors. To examine heterogeneity and clonal dynamics of tumor infiltrating lymphocytes (TILs), we applied paired single-cell RNA and TCR sequencing in three HNSCC models.

RESULTS: Anti-PD1 resistant MOC1esc1 line displayed a conserved cell intrinsic immune evasion signature. …

Subtyping Of Common Complex Diseases And Disorders By Integrating Heterogeneous Data. Identifying Clusters Among Women With Lower Urinary Tract Symptoms In The Lurn Study, Victor P. Andreev, H Henry Lai, Et Al

2020-Current year OA Pubs

We present a methodology for subtyping of persons with a common clinical symptom complex by integrating heterogeneous continuous and categorical data. We illustrate it by clustering women with lower urinary tract symptoms (LUTS), who represent a heterogeneous cohort with overlapping symptoms and multifactorial etiology. Data collected in the Symptoms of Lower Urinary Tract Dysfunction Research Network (LURN), a multi-center observational study, included self-reported urinary and non-urinary symptoms, bladder diaries, and physical examination data for 545 women. Heterogeneity in these multidimensional data required thorough and non-trivial preprocessing, including scaling by controls and weighting to mitigate data redundancy, while the various data …

Exploring The Role Of Low-Density Neutrophils During Mycobacterium Tuberculosis Infection, Ananda N Rankin, Skyler V Hendrix, Sumanta K Naik, Christina L Stallings

2020-Current year OA Pubs

Tuberculosis (TB) is caused by infection with the bacterium

Bsl2-Compliant Lethal Mouse Model Of Sars-Cov-2 And Variants Of Concern To Evaluate Therapeutics Targeting The Spike Protein, Mohanraj Manangeeswaran, Derek D C Ireland, Seth G Thacker, Ha-Na Lee, Logan Kelley-Baker, Aaron P Lewkowicz, Paul W Rothlauf, Marjorie Cornejo Pontelli, Louis-Marie Bloyet, Michael A Eckhaus, Mirian I Mendoza, Sean Whelan, Daniela Verthelyi

2020-Current year OA Pubs

Since first reported in 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is rapidly acquiring mutations, particularly in the spike protein, that can modulate pathogenicity, transmission and antibody evasion leading to successive waves of COVID19 infections despite an unprecedented mass vaccination necessitating continuous adaptation of therapeutics. Small animal models can facilitate understanding host-pathogen interactions, target selection for therapeutic drugs, and vaccine development, but availability and cost of studies in BSL3 facilities hinder progress. To generate a BSL2-compatible