Article
Multidisciplinary Sciences
Melissa Ross, Ricardo Henao, Thomas W. Burke, Emily R. Ko, Micah T. McClain, Geoffrey S. Ginsburg, Christopher W. Woods, Ephraim L. Tsalik
Summary: The study compared three host response strategies to distinguish bacterial and viral etiologies of acute respiratory illness. The gene expression signature was found to be the most accurate strategy for classifying subjects with bacterial, viral, or non-infectious ARI.
Article
Infectious Diseases
Heping Wang, Jiali Gu, Xiaonan Li, Christa E. Van der Gaast-de Jongh, Wenjian Wang, Xuehui He, Zhi Xu, Yonghong Yang, Ronald de Groot, Marien de Jonge, Yuejie Zheng
Summary: Understanding the etiology of lower respiratory tract infections is crucial for accurate diagnosis and treatment. Molecular detection methods can accurately identify a wide range of pathogens, with viral detection rates decreasing with age while atypical pathogen detection rates increasing. This approach shows promise for improving clinical outcomes in children with LRTIs.
BMC INFECTIOUS DISEASES
(2021)
Review
Biochemistry & Molecular Biology
Ewa Ostrycharz, Beata Hukowska-Szematowicz
Summary: This article presents key miRNAs involved in viral infections in humans and animals. The authors summarize existing literature data and reveal that 12 miRNAs are mainly involved in human viral infections, while 10 miRNAs are commonly found in animal viral infections. Investigating the roles of these miRNAs can contribute to understanding the pathogenesis of viral diseases and aid in the development of therapeutic agents.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Hui Li, Xiaorong Wu, Hong Zeng, Bozhen Chang, Ying Cui, Jingxiang Zhang, Ruixia Wang, Tao Ding
Summary: This study found that respiratory viral infections are associated with viral type-specific disruption of the upper respiratory microbiota. Influenza virus infections are uniquely linked with increased microbial diversity and growth rates of specific pathogens. These findings are important for understanding the differences and dynamics of respiratory microbiota in healthy participants and acute respiratory viral infections, and provide insights into the pathogenesis of viral-host-bacterial interactions for future studies on effective prevention and treatment of respiratory tract infections.
Review
Agriculture, Dairy & Animal Science
Nahed Yehia, Heba M. Salem, Yasser Mahmmod, Dalia Said, Mahmoud Samir, Sara Abdel Mawgod, Hend K. Sorour, Mona A. A. AbdelRahman, Samy Selim, Ahmed M. Saad, Mohamed T. El-Saadony, Rasha M. El-Meihy, Mohamed E. Abd El-Hack, Khaled A. El-Tarabily, Ali M. Zanaty
Summary: Many pathogens commonly infect birds through the respiratory tract, leading to respiratory disorders and significant financial losses in the poultry industry. Viral pathogens, such as avian influenza virus, Newcastle disease virus, infectious bronchitis virus, and avian pneumovirus, are particularly severe. Bacterial pathogens, including Mycoplasma gallisepticum, Staphylococcus, Bordetella avium, Pasteurella multocida, Riemerella anatipestifer, Chlamydophila psittaci, and Escherichia coli, also cause serious respiratory infections in poultry. This review provides an updated summary of the evidence for widespread poultry respiratory pathogens, along with possible control and prevention methods.
Article
Virology
Elandri Fourie, Yara E. E. Sijm, Paul Badoux, Marieke E. Merelle, Mildred E. Haverkort, Sjoerd M. Euser, Marlies A. van Houten
Summary: This study evaluated the performance and tolerability of a rhinorrhea swab in detecting viral pathogens in young children. The results showed that the rhinorrhea swab had similar efficacy in detecting viral pathogens compared to the combined swab, and it was better tolerated by both children and their parents.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Boaz Kalmovich, Daniella Rahamim-Cohen, Shirley Shapiro Ben David
Summary: Antibiotic overuse and underuse are common issues in urgent care settings due to diagnostic uncertainty. Previous clinical validation of a host-based test called MeMed BV, which distinguishes bacterial and viral infections, has prompted an examination of its impact on antibiotic prescription in a real-world setting. Results showed that physicians were more likely to prescribe antibiotics in accordance with the BV result, leading to a reduction in antibiotic prescriptions for patients with viral BV results and better antibiotic use overall.
Article
Medical Laboratory Technology
Melissa C. Remmel, Sabrina M. Coyle, Mark W. Eshoo, Timothy E. Sweeney, David C. Rawling
Summary: This study developed a rapid test system based on qRT-LAMP for profiling host gene expression from blood, which can accurately discriminate between bacterial and viral infections. The system has a short turnaround time of 12 minutes.
CLINICAL CHEMISTRY
(2022)
Article
Genetics & Heredity
Nicholas Bodkin, Melissa Ross, Micah T. McClain, Emily R. Ko, Christopher W. Woods, Geoffrey S. Ginsburg, Ricardo Henao, Ephraim L. Tsalik
Summary: In a systematic comparison of 28 host gene expression signatures, differences in performance were observed based on signature size and characteristics of the validation population, such as age and infection type. It was noted that differential performance in specific populations may only be observable through this type of large-scale validation.
Review
Allergy
Sophia Volpe, Joseph Irish, Sunny Palumbo, Eric Lee, Jacob Herbert, Ibrahim Ramadan, Eugene H. Chang
Summary: Viral infections are a common cause of upper respiratory infections and can lead to chronic rhinosinusitis. Viruses enter cells and replicate within them, while stimulating interferon-mediated immune responses. Studies suggest that viral infections may induce aberrant immune responses, resulting in loss of barrier function.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2023)
Article
Immunology
Emma M. de Koff, Marlies A. van Houten, Elisabeth A. M. Sanders, Debby Bogaert
Summary: Clinical presentation of HCoV infections in children varies, with HCoV-associated lower respiratory tract infections often co-occurring with respiratory syncytial virus and higher abundance of Haemophilus influenzae/haemolyticus. Viral and bacterial cooccurrence may drive symptoms of HCoV-associated infections.
PEDIATRIC INFECTIOUS DISEASE JOURNAL
(2021)
Article
Medicine, General & Internal
Xuhui Li, Hua Fan, Hao Zi, Hankun Hu, Binghui Li, Jiao Huang, Pengcheng Luo, Xiantao Zeng
Summary: This study aimed to estimate the global and regional burden of bacterial antimicrobial resistance (AMR) in urinary tract infections (UTI) in 2019. The results showed that globally, there were approximately 64.89 thousand deaths attributed to and 0.26 million deaths associated with bacterial AMR in UTI. Escherichia coli and Klebsiella pneumoniae had the highest resistance rates, including resistance to fluoroquinolones, carbapenems, and third-generation cephalosporins. Tailored strategies, such as enhanced surveillance and rational use of antibiotics, should be developed for different regions based on their specific pathogen-antibiotic situations and resources.
JOURNAL OF CLINICAL MEDICINE
(2022)
Article
Infectious Diseases
Manuel E. Machado-Duque, Diego Arturo Garcia, Melissa Hiromi Emura-Velez, Andres Gaviria-Mendoza, Claudia Giraldo-Giraldo, Jorge E. Machado-Alba
Summary: This study assessed the frequency of antibiotic prescriptions for patients with viral upper respiratory tract infections (URTIs) and identified variables associated with the use of antibiotics for viral infections. The study found that antibiotics were frequently prescribed inappropriately for URTIs, highlighting the need for interventions to improve their use.
Article
Immunology
Robert S. Wallis, Anne O'Garra, Alan Sher, Andreas Wack
Summary: This Perspective reflects on the historical development of host-directed immunotherapeutic interventions for viral and bacterial infections, and discusses their application to current approaches to therapy of SARS-CoV-2 and Mycobacterium tuberculosis infections.
NATURE REVIEWS IMMUNOLOGY
(2023)
Article
Infectious Diseases
Benjamin Davido, Benoit Lemarie, Elyanne Gault, Marion Pepin, Karim Jaffal, Sebastien Beaune, Lotfi Dahmane, Jennifer Dumoulin, Segolene Greffe, Djillali Annane, Pierre De Truchis
Summary: This study analyzed the predictors of outcomes in patients with viral respiratory tract infections (VRTIs) and found a significant correlation between superinfection and outcomes. The species of the virus also affects mortality rates.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Immunology
Robin Patel, Ephraim L. Tsalik, Scott Evans, Vance G. Fowler, Sarah B. Doernberg
Summary: The lack of a gold standard poses challenges in evaluating the accuracy of diagnostic tests for infectious diseases. Various approaches, such as multitest comparators and clinically adjudicated reference standards, can be used to overcome this challenge.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Medicine, General & Internal
Chuan Hong, Michael J. J. Pencina, Daniel M. M. Wojdyla, Jennifer L. L. Hall, Suzanne E. E. Judd, Michael Cary, Matthew M. M. Engelhard, Samuel Berchuck, Ying Xian, Ralph D'Agostino Sr, George Howard, Brett Kissela, Ricardo Henao
Summary: This study compared the performance of stroke-specific algorithms with pooled cohort equations for the prediction of new-onset stroke across different subgroups. The existing stroke-specific risk prediction models and novel machine learning techniques did not significantly improve discriminative accuracy for new-onset stroke compared with the pooled cohort equations, and the REGARDS self-report model had the best calibration.
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
(2023)
Article
Multidisciplinary Sciences
Julie M. Steinbrink, Cameron Miller, Rachel A. Myers, Scott Sanoff, Anna Mazur, Thomas W. Burke, Jennifer Byrns, Annette M. Jackson, Xunrong Luo, Micah T. McClain
Summary: Renal transplantation from HCV NAAT-positive donors to uninfected recipients increases the organ donation pool but may cause adverse outcomes due to dysregulated immunologic activation. In this study, gene expression patterns in circulating leukocytes were evaluated to understand the immune dysregulation and predict clinical outcomes. HCV infection incited a marked transcriptomic response in renal transplant recipients, reflecting antiviral immune pathways, which resolved after sustained viral response. Differential gene expression was noted in patients with CMV DNAemia or allograft rejection, although accurate predictive classifiers were not developed. Acute HCV infection induces immune activation in the presence of immunosuppression, which resolves after antiviral therapy. Changes in gene expression patterns are associated with clinical outcomes, but larger studies are needed for accurate predictions.
Article
Computer Science, Interdisciplinary Applications
Junya Chen, Matthew Engelhard, Ricardo Henao, Samuel Berchuck, Brian Eichner, Eliana M. Perrin, Guillermo Sapiro, Geraldine Dawson
Summary: Recent work has demonstrated that predictive models based on structured electronic health record (EHR) data can stratify the likelihood of autism from an early age. This study aimed to improve the accuracy of early autism prediction by integrating clinical narratives with structured EHR data. Models were built separately using the two types of data and then combined into an ensemble model. The results showed that the ensemble model had superior performance, achieving promising accuracy within 30 days and outperforming models based on structured data alone.
JOURNAL OF BIOMEDICAL INFORMATICS
(2023)
Article
Geriatrics & Gerontology
Juliessa M. Pavon, Laura Previll, Myung Woo, Ricardo Henao, Mary Solomon, Ursula Rogers, Andrew Olson, Jonathan Fischer, Christopher Leo, Gerda Fillenbaum, Helen Hoenig, David Casarett
Summary: A machine learning algorithm using electronic health record (EHR) data was developed and evaluated for identifying functional impairment. With the use of 11 EHR clinical variable domains and a supervised machine learning algorithm, it was able to accurately distinguish functional status states. Important features in predicting functional status included age, falls, hospitalization, home health use, labs, comorbidities, and social determinants of health.
JOURNAL OF THE AMERICAN GERIATRICS SOCIETY
(2023)
Article
Gastroenterology & Hepatology
Benjamin V. Tran, Dimitrios Moris, Daniela Markovic, Hamed Zaribafzadeh, Ricardo Henao, Quirino Lai, Sander S. Florman, Parissa Tabrizian, Brandy Haydel, Richard M. Ruiz, Goran B. Klintmalm, David D. Lee, C. Burcin Taner, Maarouf Hoteit, Matthew H. Levine, Umberto Cillo, Alessandro Vitale, Elizabeth C. Verna, Karim J. Halazun, Amit D. Tevar, Abhinav Humar, William C. Chapman, Neeta Vachharajani, Federico Aucejo, Jan Lerut, Olga Ciccarelli, Mindie H. Nguyen, Marc L. Melcher, Andre Viveiros, Benedikt Schaefer, Maria Hoppe-Lotichius, Jens Mittler, Trevor L. Nydam, James F. Markmann, Massimo Rossi, Constance Mobley, Mark Ghobrial, Alan N. Langnas, Carol A. Carney, Jennifer Berumen, Gabriel T. Schnickel, Debra L. Sudan, Johnny C. Hong, Abbas Rana, Christopher M. Jones, Thomas M. Fishbein, Ronald W. Busuttil, Andrew S. Barbas, Vatche G. Agopian
Summary: The individual prediction of post-liver transplantation hepatocellular carcinoma (HCC) recurrence risk is important. By analyzing the data of 4981 HCC patients undergoing transplantation, a prediction score was developed to accurately discriminate the risk of HCC recurrence. The score was externally validated in another 1160 patients, showing consistent results in risk discrimination.
LIVER TRANSPLANTATION
(2023)
Article
Pathology
Serge Assaad, David Dov, Richard Davis, Shahar Kovalsky, Walter T. Lee, Russel Kahmke, Daniel Rocke, Jonathan Cohen, Ricardo Henao, Lawrence Carin, Danielle Elliott Range
Summary: This study evaluated the performance of deep learning models in classifying thyroid fine-needle aspiration biopsies using microscope images captured with a high-resolution scanner and a mobile phone camera. The baseline machine learning algorithm performed poorly on mobile images compared to scanner images, but the performance gap was reduced by applying color augmentation during training. The model showed accurate predictions of Bethesda categories and required a small number of ROIs for optimal performance.
Correction
Multidisciplinary Sciences
Nicholas S. Giroux, Shengli Ding, Micah T. McClain, Thomas W. Burke, Elizabeth Petzold, Hong A. Chung, Grecia O. Rivera, Ergang Wang, Rui Xi, Shree Bose, Tomer Rotstein, Bradly P. Nicholson, Tianyi Chen, Ricardo Henao, Gregory D. Sempowski, Thomas N. Denny, Maria Iglesias De Ussel, Lisa L. Satterwhite, Emily R. Ko, Geoffrey S. Ginsburg, Bryan D. Kraft, Ephraim L. Tsalik, Xiling Shen, Christopher W. Woods
SCIENTIFIC REPORTS
(2023)
Article
Computer Science, Artificial Intelligence
Paidamoyo Chapfuwa, Chenyang Tao, Chunyuan Li, Irfan Khan, Karen J. Chandross, Michael J. Pencina, Lawrence Carin, Ricardo Henao
Summary: Models for predicting the time of a future event are crucial for risk assessment. We propose neural time-to-event models that account for calibration and uncertainty while predicting accurate absolute event times.
IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS
(2023)
Article
Immunology
Stephen P. Bergin, Roy F. Chemaly, Sanjeet S. Dadwal, Joshua A. Hill, Yeon Joo Lee, Ghady Haidar, Alfred Luk, Alexander Drelick, Peter Chin-Hong, Esther Benamu, Fareed Khawaja, Deepa Nanayakkara, Genovefa A. Papanicolaou, Catherine Butkus Small, Monica Fung, Michelle A. Barron, Thomas Davis, Micah T. Mcclain, Eileen K. Maziarz, Deng B. Madut, Armando D. Bedoya, Daniel L. Gilstrap, Jamie L. Todd, Christina E. Barkauskas, Robert Bigelow, Jeffrey D. Leimberger, Ephraim L. Tsalik, Olivia Wolf, Mona Mughar, Desiree Hollemon, Radha Duttagupta, Daniel S. Lupu, Sivan Bercovici, Bradley A. Perkins, Timothy A. Blauwkamp, Vance G. Fowler, Thomas L. Holland
Summary: Non-invasive plasma microbial cell-free DNA sequencing significantly increased diagnostic yield in immunocompromised patients with pneumonia undergoing bronchoscopy and extensive microbiologic and molecular testing.
CLINICAL INFECTIOUS DISEASES
(2023)
Proceedings Paper
Computer Science, Artificial Intelligence
Vinay Kumar Verma, Nikhil Mehta, Shijing Si, Ricardo Henao, Lawrence Carin
Summary: Weight pruning is a popular approach for compressing deep convolutional neural networks. The proposed Structured Sparse Convolution (SSC) leverages the inherent structure in images to reduce the parameters in the convolutional filter, resulting in improved efficiency compared to existing methods. Extensive experiments show that architectures based on SSC achieve state-of-the-art performance on various classification benchmarks.
2023 IEEE/CVF WINTER CONFERENCE ON APPLICATIONS OF COMPUTER VISION (WACV)
(2023)
Article
Ophthalmology
Eduardo B. Mariottoni, Shounak Datta, Leonardo S. Shigueoka, Alessandro A. Jammal, Ivan M. Tavares, Ricardo Henao, Lawrence Carin, Felipe A. Medeiros
Summary: This study developed and validated a deep learning model to detect glaucoma progression using spectral-domain OCT measurements of retinal nerve fiber layer thickness. The DL model showed high diagnostic performance and outperformed conventional trend-based analyses. This model provides a promising approach for assessing glaucomatous structural progression.
OPHTHALMOLOGY GLAUCOMA
(2023)
Article
Biochemical Research Methods
Zijun Zhang, Natalie Sauerwald, Antonio Cappuccio, Irene Ramos, Venugopalan D. Nair, German Nudelman, Elena Zaslavsky, Yongchao Ge, Angelo Gaitas, Hui Ren, Joel Brockman, Jennifer Geis, Naveen Ramalingam, David King, Micah T. McClain, Christopher W. Woods, Ricardo Henao, Thomas W. Burke, Ephraim L. Tsalik, Carl W. Goforth, Rhonda A. Lizewski, Stephen E. Lizewski, Dawn L. Weir, Andrew G. Letizia, Stuart C. Sealfon, Olga G. Troyanskaya
Summary: Assays detecting blood transcriptome changes are studied for infectious disease diagnosis. Blood-based RNA alternative splicing (AS) events have the potential to be better diagnostic biomarkers compared to gene expression. This study presents a computational framework for developing AS diagnostic biomarkers using SARS-CoV-2 infection data and identifies a major functional AS program switch upon viral infection. AS-based biomarkers are more accurate for SARS-CoV-2 diagnosis compared to transcriptome signatures, and microfluidic PCR diagnostic assays achieve nearly perfect test accuracy.
CELL REPORTS METHODS
(2023)
Meeting Abstract
Obstetrics & Gynecology
Johanna Quist-Nelson, Marie Louise Meng, Jennifer J. Stuart, Matthew Fuller, Ursula Rogers, Michael Pencina, Janet Rich-Edwards, Ricardo Henao
AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY
(2023)
