Browsing by Author "Weaver, Jessica"

Now showing 1 - 4 of 4
  • Thumbnail Image
    Item
    Application of unsupervised deep learning algorithms for identification of specific clusters of chronic cough patients from EMR data
    (BMC, 2022-04-19) Shao, Wei; Luo, Xiao; Zhang, Zuoyi; Han, Zhi; Chandrasekaran, Vasu; Turzhitsky, Vladimir; Bali, Vishal; Roberts, Anna R.; Metzger, Megan; Baker, Jarod; La Rosa, Carmen; Weaver, Jessica; Dexter, Paul; Huang, Kun; Biostatistics and Health Data Science, School of Medicine
    Background: Chronic cough affects approximately 10% of adults. The lack of ICD codes for chronic cough makes it challenging to apply supervised learning methods to predict the characteristics of chronic cough patients, thereby requiring the identification of chronic cough patients by other mechanisms. We developed a deep clustering algorithm with auto-encoder embedding (DCAE) to identify clusters of chronic cough patients based on data from a large cohort of 264,146 patients from the Electronic Medical Records (EMR) system. We constructed features using the diagnosis within the EMR, then built a clustering-oriented loss function directly on embedded features of the deep autoencoder to jointly perform feature refinement and cluster assignment. Lastly, we performed statistical analysis on the identified clusters to characterize the chronic cough patients compared to the non-chronic cough patients. Results: The experimental results show that the DCAE model generated three chronic cough clusters and one non-chronic cough patient cluster. We found various diagnoses, medications, and lab tests highly associated with chronic cough patients by comparing the chronic cough cluster with the non-chronic cough cluster. Comparison of chronic cough clusters demonstrated that certain combinations of medications and diagnoses characterize some chronic cough clusters. Conclusions: To the best of our knowledge, this study is the first to test the potential of unsupervised deep learning methods for chronic cough investigation, which also shows a great advantage over existing algorithms for patient data clustering.
  • Thumbnail Image
    Item
    Management of Chronic Cough in Adult Primary Care: A Qualitative Study
    (Springer, 2021-09) Gowan, Tayler M.; Huffman, Monica; Weiner, Michael; Talib, Tasneem L.; Schelfhout, Jonathan; Weaver, Jessica; Griffith, Ashley; Doshi, Ishita; Dexter, Paul; Bali, Vishal; Medicine, School of Medicine
    This study is the first to describe, qualitatively, PCPs’ experiences evaluating and treating CC in adults. By interviewing clinicians, we sought to understand reasons for referrals, accessibility and use of clinical guidelines, confidence in evaluation and treatment, perceptions and attitudes, and desired resources. Findings may help in elucidating clinical decision-making and could indicate areas for improvement in dissemination and use of guidelines.
  • Thumbnail Image
    Item
    Neutrophils Resist Ferroptosis and Promote Breast Cancer Metastasis through Aconitate Decarboxylase 1
    (Elsevier, 2023) Zhao, Yun; Liu, Zhongshun; Liu, Guoqiang; Zhang, Yuting; Liu, Sheng; Gan, Dailin; Chang, Wennan; Peng, Xiaoxia; Sung, Eun Suh; Gilbert, Keegan; Zhu, Yini; Wang, Xuechun; Zeng, Ziyu; Baldwin, Hope; Ren, Guanzhu; Weaver, Jessica; Huron, Anna; Mayberry, Toni; Wang, Qingfei; Wang, Yujue; Diaz-Rubio, Maria Elena; Su, Xiaoyang; Stack, M. Sharon; Zhang, Siyuan; Lu, Xuemin; Sheldon, Ryan D.; Li, Jun; Zhang, Chi; Wan, Jun; Lu, Xin; Medical and Molecular Genetics, School of Medicine
    Metastasis causes breast cancer-related mortality. Tumor-infiltrating neutrophils (TINs) inflict immunosuppression and promote metastasis. Therapeutic debilitation of TINs may enhance immunotherapy, yet it remains a challenge to identify therapeutic targets highly expressed and functionally essential in TINs but under-expressed in extra-tumoral neutrophils. Here, using single-cell RNA sequencing to compare TINs and circulating neutrophils in murine mammary tumor models, we identified aconitate decarboxylase 1 (Acod1) as the most upregulated metabolic enzyme in mouse TINs and validated high Acod1 expression in human TINs. Activated through the GM-CSF-JAK/STAT5-C/EBPβ pathway, Acod1 produces itaconate, which mediates Nrf2-dependent defense against ferroptosis and upholds the persistence of TINs. Acod1 ablation abates TIN infiltration, constrains metastasis (but not primary tumors), bolsters antitumor T cell immunity, and boosts the efficacy of immune checkpoint blockade. Our findings reveal how TINs escape from ferroptosis through the Acod1-dependent immunometabolism switch and establish Acod1 as a target to offset immunosuppression and improve immunotherapy against metastasis.
  • Thumbnail Image
    Item
    Prescriptions of opioid-containing drugs in patients with chronic cough
    (Sage, 2024) Weiner, Michael; Liu, Ziyue; Schelfhout, Jonathan; Dexter, Paul; Roberts, Anna R.; Griffith, Ashley; Bali, Vishal; Weaver, Jessica; Biostatistics and Health Data Science, Richard M. Fairbanks School of Public Health
    Background: Chronic cough (CC) affects about 10% of adults, but opioid use in CC is not well understood. Objectives: To determine the use of opioid-containing cough suppressant (OCCS) prescriptions in patients with CC using electronic health records. Design: Retrospective cohort study. Methods: Through retrospective analysis of Midwestern U.S. electronic health records, diagnoses, prescriptions, and natural language processing identified CC - at least three medical encounters with cough, with 56-120 days between first and last encounter - and a 'non-chronic cohort'. Student's t-test, Pearson's chi-square, and zero-inflated Poisson models were used. Results: About 20% of 23,210 patients with CC were prescribed OCCS; odds of an OCCS prescription were twice as great in CC. In CC, OCCS drugs were ordered in 38% with Medicaid insurance and 15% with commercial insurance. Conclusion: Findings identify an important role for opioids in CC, and opportunity to learn more about the drugs' effectiveness.