Article
Medicine, General & Internal
Raquel Almansa, Carmen Herrero-Rodriguez, Misericordia Martinez-Huelamo, Maria del Pilar Vicente-Andres, Jose Angel Nieto-Barbero, Miryam Martin-Ballesteros, Maria del Mar Rodilla-Carvajal, Amanda de la Fuente, Alicia Ortega, Maria Jesus Alonso-Ramos, James Wacker, Oliver Liesenfeld, Timothy E. Sweeney, Jesus F. Bermejo-Martin, Luis Garcia-Ortiz
Summary: The Fever-7 test is a promising host immune mRNA marker for the early identification of respiratory viral infections in the community, showing high sensitivity and specificity in predicting viral infections.
EUROPEAN JOURNAL OF CLINICAL INVESTIGATION
(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)
Review
Public, Environmental & Occupational Health
Yiming Chen, Yuelin Wang, Ningbin Quan, Jun Yang, Yinyin Wu
Summary: Wearing masks can effectively prevent respiratory viral infections. Sensitivity analysis shows that the results are robust and reliable, with no significant publication bias in case-control studies and most subgroup analyses.
FRONTIERS IN PUBLIC HEALTH
(2022)
Review
Cell Biology
Spiros Vlahopoulos, Ke Wang, Yaoyao Xue, Xu Zheng, Istvan Boldogh, Lang Pan
Summary: The bronchial vascular endothelial network plays crucial roles in pulmonary pathology during respiratory viral infections, and the lack of effective vaccines and antiviral drugs poses obstacles in disease prevention. Current management of these infections is limited to supportive clinical care, with respiratory failure as the primary cause of morbidity and mortality. Endothelial complications such as edema also contribute significantly to the disease burden.
Review
Biochemistry & Molecular Biology
Pawel Franczuk, Michal Tkaczyszyn, Maria Kulak, Esabel Domenico, Piotr Ponikowski, Ewa Anita Jankowska
Summary: Viral respiratory infections (VRI) are common and can worsen existing cardiovascular diseases and lead to new complications, especially in COVID-19.
Article
Biochemistry & Molecular Biology
Judy Bai, Katherine Ma, Shangyang Xia, Richard Geng, Claire Shen, Limin Jiang, Xi Gong, Hui Yu, Shuguang Leng, Yan Guo
Summary: This study explores the differences in mutational signatures between different races and their association with environmental pollutant exposures. It shows that increased pollution levels are associated with worse cancer prognosis and that Asians may have a genetic or genomic disadvantage concerning aflatoxin exposure.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Medicine, Research & Experimental
Khadijeh Koushki, Maryam Salemi, Seyed Mohammad Miri, Yaser Arjeini, Mohsen Keshavarz, Amir Ghaemi
Summary: The expansion of myeloid-derived suppressor cells (MDSCs) is enhanced during pathological conditions such as viral respiratory infections, with evidence showing an accumulation of MDSCs in severe stages of COVID-19. MDSCs delay virus clearance through inhibiting T-cell responses, leading to significant pathogenic effects on severe forms of COVID-19. Targeting MDSCs may help reactivate T-cell immunity to prevent severe stages of the disease.
BIOMEDICINE & PHARMACOTHERAPY
(2021)
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
Virology
Guohong Zhu, Dan Xu, Yuanyuan Zhang, Tianlin Wang, Lingyan Zhang, Weizhong Gu, Meiping Shen
Summary: The study found that the rates of viral infection in children vary by different ages and seasons, with the highest positivity rate of adenovirus appearing in the preschool period, respiratory syncytial virus being highest in infants, and influenza virus increasing with age. The total positive rate of viral infection in different seasons is highest in winter, with influenza positivity rate also being highest in winter.
Review
Immunology
Coen Govers, Philip C. Calder, Huub F. J. Savelkoul, Ruud Albers, R. J. Joost van Neerven
Summary: Respiratory infections, especially in vulnerable groups, place a heavy burden on the health care system. Nutrition plays a role in optimizing immune responsiveness and preventing infections. Micronutrients act as regulators of immune cells' molecular responses, while undernutrition and specific micronutrient deficiencies impair immune response and increase susceptibility to respiratory and gastrointestinal infections. Dietary components such as proteins, pre-, pro- and synbiotics, as well as animal- and plant-derived bioactive components, can support the immune system. Both innate and adaptive defense systems contribute to respiratory tract immunity, and this review aims to describe the effects of different dietary components on these immune responses.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Immunology
SuHyeon Oh, SangJoon Lee
Summary: Innate immunity is a crucial defense against pathogens, including viruses, and ZBP1 plays a central role in regulating inflammatory cell death during viral infection. By sensing viral RNA, ZBP1 induces PANoptosis to protect host cells, but some viruses, like coronaviruses, can exploit this process to cause harm to the host. Understanding the molecular mechanism of ZBP1-derived PANoptosis is important for improving therapeutic strategies.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Allergy
Berber Vlieg-Boerstra, Nicolette de Jong, Rosan Meyer, Carlo Agostoni, Valentina De Cosmi, Kate Grimshaw, Gregorio Paolo Milani, Antonella Muraro, Hanneke Oude Elberink, Isabella Pali-Scholl, Caroline Roduit, Mari Sasaki, Isabel Skypala, Milena Sokolowska, Marloes van Splunter, Eva Untersmayr, Carina Venter, Liam O'Mahony, Bright Nwaru
Summary: Nutrient supplementation for the general population appears to have limited effectiveness in preventing respiratory tract infections, with zinc supplementation showing potential protective effects in children in Asia and vitamin D supplementation reducing the incidence of RTIs in adults in North America.
Review
Immunology
Iole Macchia, Valentina La Sorsa, Francesca Urbani, Sonia Moretti, Caterina Antonucci, Claudia Afferni, Giovanna Schiavoni
Summary: Eosinophils are important in allergic asthma and parasitic infections, but they also participate in the immune response against respiratory viruses. In the context of COVID-19, eosinophils can serve as potential biomarkers for diagnosis, prognosis, and severity prediction. This review provides an overview of the role of eosinophils in various respiratory viral infections and discusses their utility as prognostic/predictive immune biomarkers in emerging respiratory viral diseases, particularly COVID-19.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Pharmacology & Pharmacy
Mehwish Jabeen, Melody Dutot, Roxane Fagon, Bernard Verrier, Claire Monge
Summary: Natural marine sulfated polysaccharides with promising antiviral activity could be a safe alternative to synthetic broad-spectrum antiviral drugs.
Review
Virology
Justine Oliva, Olivier Terrier
Summary: Respiratory tract infections pose a significant public health problem, with viral-bacterial co-infections playing a key role in the severity of these infections. Understanding the mechanisms of these co-infections at physiological and immunological levels is crucial, as well as exploring the importance of the microbiome and pathological context in the evolution of co-infections.
Article
Mathematical & Computational Biology
Debashis Ghosh, Michael S. Sabel
Summary: This study introduces a weighting approach using convex optimization to transfer information and develop prediction-guided analyses by incorporating information from external risk calculators to local datasets. It also utilizes tree structures to describe 'calculator-guided observations' and sheds light on the potential transferability of external calculators to local datasets.
STATISTICS IN BIOSCIENCES
(2022)
Article
Computer Science, Interdisciplinary Applications
Youngjoo Cho, Xiang Zhan, Debashis Ghosh
Summary: In clinical trials, individuals in different subgroups may have different treatment effects, highlighting the importance of considering individual differences in treatment benefit. This study introduces the concept of predictive directions and validates its utility through simulation studies and real data analysis.
COMPUTATIONAL STATISTICS & DATA ANALYSIS
(2022)
Article
Biochemical Research Methods
Souvik Seal, Debashis Ghosh
Summary: This study presents a new method for analyzing the interaction of proteins or markers in the tumor microenvironment of cancer patients, finding co-expression to be associated with disease risk and survival, and demonstrating the robustness of the method.
Article
Chemistry, Analytical
Cameron Severn, Krithika Suresh, Carsten Gorg, Yoon Seong Choi, Rajan Jain, Debashis Ghosh
Summary: Machine learning models have shown remarkable accuracy in predicting clinical factors from medical imaging, but their lack of interpretability has been a concern. Explainable machine learning methods, such as Shapley values, can help explain the behavior of these models and identify important predictors. Incorporating these methods into medical software can increase trust in machine learning predictions and assist physicians in making important decisions. This article presents a novel pipeline for explainable medical imaging using radiomics data and Shapley values, and demonstrates its application in predicting a genetic mutation from MRI data.
Article
Mathematical & Computational Biology
Kevin P. Josey, Fan Yang, Debashis Ghosh, Sridharan Raghavan
Summary: Proper evaluations of internal and external validity are important in clinical research studies. Randomized clinical trials can address internal validity but may lack external validity. Large prospective observational studies may have external validity but are susceptible to threats to internal validity. Methods that address confounding and enhance transportability of study results across populations are crucial for valid causal inference.
STATISTICS IN MEDICINE
(2022)
Article
Biochemical Research Methods
Thao Vu, Julia Wrobel, Benjamin G. Bitler, Erin L. Schenk, Kimberly R. Jordan, Debashis Ghosh
Summary: Investigating spatial patterns and interactions of cells in the tumor microenvironment (TME) provides useful insights into cancer development and progression. In this work, we proposed a novel approach which combined established spatial summary functions with functional data analysis to flexibly model the cell-cell interactions with overall survival at different inter-cell distances, in conjunction with other clinical predictors such as age, disease stage. By applying the proposed framework to multiplex immunohistochemistry (mIHC) data of patients with non-small cell lung cancer (NSCLC), we studied the nonlinear impact of spatial interactions between tumor and stromal cells on overall survival. The applicability of our proposed method is further validated using a publicly available multiplexed ion beam imaging (MIBI) triple-negative breast cancer (TNBC) dataset.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Clinical Neurology
Lorraine Flet-Berliac, Nicolas Tchitchek, Anne Lepine, Anca Florea, Helene Maurey, Pascale Chretien, Salima Hacein-Bey-Abina, Frederic Villega, Emmanuel Cheuret, Veronique Rogemond, Geraldine Picard, Jerome Honnorat, Kumaran Deiva
Summary: This French study aimed to investigate the long-term clinical and cognitive outcomes of patients with anti-N-methyl-D-aspartate receptor encephalitis (NMDAR-E). The study found that more than 45% of patients experienced cognitive and academic difficulties, and the severity of symptoms seemed to have an impact on cognition and academic performances.
DEVELOPMENTAL MEDICINE AND CHILD NEUROLOGY
(2023)
Article
Rheumatology
Marie Binvignat, Gabriel Pires, Nicolas Tchitchek, Felicie Costantino, Alice Courties, David Klatzmann, Atul J. Butte, Bernard Combe, Maxime Dougados, Pascal Richette, Encarnita Mariotti-Ferrandiz, Francis Berenbaum, Jeremie Sellam
Summary: This study aimed to classify phenotypes in hand osteoarthritis (HOA) based on cardinal symptoms. Using the Australian/Canadian Osteoarthritis Hand Index (AUSCAN) subscores and visual analog scale, a hierarchical agglomerative clustering analysis was performed on data from the Digital Cohort Design (DIGICOD). Five clusters were identified, indicating different levels of symptoms and associations with joint destruction and physical/psychological burden.
ARTHRITIS CARE & RESEARCH
(2023)
Article
Oncology
Shuozhi Zuo, Kevin P. Josey, Sridharan Raghavan, Fan Yang, Elizabeth Juarez-Colunga, Debashis Ghosh
Summary: Differences in treatment effects were observed in 12 randomized phase III colon cancer adjuvant clinical trials. The reasons for these differences were investigated and it was found that they may be due to the distribution of unobserved covariates or study-level features.
JCO CLINICAL CANCER INFORMATICS
(2022)
Article
Multidisciplinary Sciences
Yonghua Zhuang, Fuyong Xing, Debashis Ghosh, Brian D. D. Hobbs, Craig P. P. Hersh, Farnoush Banaei-Kashani, Russell P. P. Bowler, Katerina Kechris
Summary: Network approaches have been used to study the complex mechanisms of diseases like COPD. However, integrating protein-protein interaction (PPI) network information with omics data for disease prediction is still limited. This study uses a deep learning method called ConvGNN to integrate COPD-associated PPI, proteomics, and transcriptomics data and improve the accuracy of COPD classification. The updated COPD-associated network developed using AhGlasso algorithm further enhances prediction accuracy. Gene Ontology enrichment analysis identifies important gene/proteins and signaling pathways for COPD classifications.
Article
Medicine, General & Internal
Eric W. Prince, Debashis Ghosh, Carsten Gorg, Todd C. Hankinson
Summary: Diagnosis of ACP mainly relies on invasive pathological examination, although clinical experts can distinguish it from MRI with an accuracy of 86%. Deep learning classification provides a potential non-invasive diagnostic solution, but its implementation is limited due to the lack of predictive uncertainty representation.
Article
Endocrinology & Metabolism
Randi K. Johnson, Amanda J. Ireton, Patrick M. Carry, Lauren A. Vanderlinden, Fran Dong, Alex Romero, David R. Johnson, Debashis Ghosh, Fan Yang, Brigitte Frohnert, Ivana V. Yang, Katerina Kechris, Marian Rewers, Jill M. Norris
Summary: This study examined the association between T1D family history and T1D risk mediated by methylation near the DLGAP2 gene. The results showed a significant interaction between T1D family history and methylation at DLGAP2 region CpGs on T1D risk. The increased risk of T1D for children with affected mothers compared to those with no family history was mediated through differences in methylation at two CpGs in the DLGAP2 region, while DNA methylation changes did not explain the increased risk for children with an affected father or sibling. Additionally, DNA methylation in the DLGAP2 region was associated with gene expression of nearby protein-coding genes.
PEDIATRIC DIABETES
(2023)
Article
Genetics & Heredity
Souvik Seal, Benjamin G. Bitler, Debashis Ghosh
Summary: This article introduces a non-parametric method called SMASH for detecting spatially variable genes in high-throughput spatial transcriptomics studies. Compared with other methods, SMASH has superior statistical power and robustness, and can be applied to datasets from different platforms, helping to uncover the structural and functional characteristics of tissues.
Article
Statistics & Probability
Youngjoo Cho, Paul L. Auer, Debashis Ghosh
Summary: Mendelian Randomization is a popular method used in genomic studies to estimate causal effects. This paper focuses on IV selection and introduces nonparametric variable selection approaches, comparing linear and nonlinear instrumental variable selection methods. Simulation studies demonstrate the good performance of the proposed methods, which are also applied to the UKBiobank data for Mendelian Randomization.
SANKHYA-SERIES B-APPLIED AND INTERDISCIPLINARY STATISTICS
(2023)
Article
Critical Care Medicine
Antoine Monsel, Caroline Hauw-Berlemont, Miryam Mebarki, Nicholas Heming, Julien Mayaux, Otriv Nguekap Tchoumba, Jean-Luc Diehl, Alexandre Demoule, Djillali Annane, Clemence Marois, Sophie Demeret, Emmanuel Weiss, Guillaume Voiriot, Muriel Fartoukh, Jean-Michel Constantin, Bruno Megarbane, Gaetan Plantefeve, Stephanie Malard-Castagnet, Sonia Burrel, Michelle Rosenzwajg, Nicolas Tchitchek, Helene Boucher-Pillet, Guillaume Churlaud, Audrey Cras, Camille Maheux, Chloe Pezzana, Mamadou Hassimiou Diallo, Jacques Ropers, Philippe Menasche, Jerome Larghero
Summary: The efficacy of UC-MSCs in patients with SARS-CoV-2-induced ARDS was assessed in this study. The results showed no significant difference in respiratory indicators between the UC-MSCs and placebo groups. The repeated UC-MSCs infusions did not lead to any serious adverse events during treatment or thereafter.