Article
Critical Care Medicine
Ana I. Hernandez Cordero, Chen Xi Yang, Julia Yang, Steve Horvath, Tawimas Shaipanich, Julia MacIsaac, David T. S. Lin, Michael S. Kobor, Silvia Guillemi, Marianne Harris, Wan Lam, Stephen Lam, Julio Montaner, S. F. Paul Man, Don D. Sin, Janice M. Leung
Summary: By analyzing the DNA methylation and gene expression of bronchial epithelial brushings from PLWH, it was found that methylation age acceleration and shorter methylation estimates of telomere length were observed in PLWH with COPD, which may contribute to the increased risk of COPD in this population. The distinct methylation profile of PLWH with COPD, different from that of patients with COPD alone, suggests a unique pathogenesis for HIV-associated COPD.
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2022)
Review
Medicine, General & Internal
Stephanie A. Christenson, Benjamin M. Smith, Mona Bafadhel, Nirupama Putcha
Summary: Chronic obstructive pulmonary disease (COPD) is a global health problem that leads to high morbidity, mortality, and healthcare utilization. Its main causes are exposure to harmful particles, such as tobacco smoke and pollutants. Recent research has shown that various factors throughout the life course increase the risk of developing COPD. Innovations in omics and imaging techniques have provided greater understanding of the disease's pathophysiology, potentially leading to advancements in its prevention, diagnosis, and treatment. This review focuses on recent advances in the epidemiology, pathophysiology, imaging, diagnosis, and treatment of COPD.
Article
Medicine, Research & Experimental
Yonghong Wu, Zhou Luo, Chuntao Liu
Summary: This study identified differences in fecal microbiome abundance and composition in AECOPD patients compared to stable COPD patients and normal subjects. The variations in fecal microbiota may be associated with the progression of COPD.
Article
Biochemical Research Methods
S. M. Hasan Mahmud, Md Al-Mustanjid, Farzana Akter, Md Shazzadur Rahman, Kawsar Ahmed, Md Habibur Rahman, Wenyu Chen, Mohammad Ali Moni
Summary: COVID-19 poses a current threat to humanity, especially to individuals with risk factors such as IPF and COPD. By conducting transcriptomic analysis, researchers identified common pathways and molecular biomarkers in IPF, COPD, and COVID-19 to enhance understanding of their connection. The study also revealed potential candidate drugs for effective COVID-19 therapeutic interventions.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Fei Wang, Boxin Yang, Jiao Qiao, Linlu Bai, Zijing Li, Wenyuan Sun, Qi Liu, Shuo Yang, Liyan Cui
Summary: This study aimed to identify biomarkers for the quick and accurate diagnosis of AECOPD. The results showed that serum exosomal miR-1258 had the highest correlation with AECOPD diagnosis and had superior discriminatory ability compared to other biomarkers. Combining exosomal miR-1258 with NLR further improved the diagnostic accuracy. The logistic regression model based on miR-1258, NLR, and neutrophil count had the highest accuracy in distinguishing AECOPD from SCOPD.
SCIENTIFIC REPORTS
(2023)
Article
Critical Care Medicine
Carlos Cabrera Lopez, Alejandra Sanchez Santos, Angelina Lemes Castellano, Sara Cazorla Rivero, Joaquin Brena Atienza, Enrique Gonzalez Davila, Bartolome Celli, Ciro Casanova Macario
Summary: Differences in the subtypes of circulating eosinophils between patients with asthma and those with COPD were found. This could have clinical implications in the interpretation of eosinophil significance and the approach to therapy in these patients.
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2023)
Article
Critical Care Medicine
Min Hyung Ryu, Jeong H. Yun, Jarrett D. Morrow, Aabida Saferali, Peter Castaldi, Robert Chase, Meryl Stav, Zhonghui Xu, Igor Barjaktarevic, MeiLan Han, Wassim Labaki, Yvonne J. Huang, Stephanie Christenson, Wanda O'Neal, Russell Bowler, Don D. Sin, Christine M. Freeman, Jeffrey L. Curtis, Craig P. Hersh
Summary: This study found a correlation between the transcriptome of circulating leukocytes and exacerbations of chronic obstructive pulmonary disease (COPD). Patients with decreased CD4 T cells in their blood were more susceptible to exacerbations. These findings provide new insights into the pathogenesis of COPD and potential strategies for its treatment and management.
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2023)
Article
Medicine, Research & Experimental
Jessica Nouws, Feng Wan, Eric Finnemore, Willy Roque, So-Jin Kim, Isabel Bazan, Chuan-xing Li, C. Magnus Skold, Qile Dai, Xiting Yan, Maurizio Chioccioli, Veronique Neumeister, Clemente J. Britto, Joann Sweasy, Ranjit Bindra, Asa M. Wheelock, Jose L. Gomez, Naftali Kaminski, Patty J. Lee, Maor Sauler
Summary: The microRNA miR-24-3p plays a vital role in regulating cellular stress responses in the pathogenesis of chronic obstructive pulmonary disease (COPD), with its decrease leading to increased susceptibility to emphysema and affecting disease severity through increased BIM and apoptosis.
Article
Biochemistry & Molecular Biology
Stanislav Kotlyarov, Anna Kotlyarova
Summary: Smoking can influence the expression of the ABCA1 gene, thereby modulating lipid transport processes in macrophages which are part of the mechanisms of inflammation development in chronic obstructive pulmonary disease (COPD).
Review
Biotechnology & Applied Microbiology
Tarun Virmani, Girish Kumar, Reshu Virmani, Ashwani Sharma, Kamla Pathak
Summary: This article provides updated information on the treatment of COPD, with a focus on nanocarrier-based approaches and the potential of gene therapy and stem cell therapy to combat COPD.
Article
Medicine, Research & Experimental
Caspar Schiffers, Cheryl van de Wetering, Robert A. Bauer, Aida Habibovic, Milena Hristova, Christopher M. Dustin, Sara Lambrichts, Pamela M. Vacek, Emiel F. M. Wouters, Niki L. Reynaert, Albert van der Vliet
Summary: The downregulation of DUOX1 in the airways of patients with Chronic Obstructive Pulmonary Disease (COPD) may contribute to the pathogenesis of COPD, leading to airway remodeling and emphysema. Animal studies also demonstrate that Duox1 deficiency exacerbates lung pathology induced by smoke exposure.
Article
Biochemistry & Molecular Biology
Jonas Eriksson Strom, Simon Kebede Merid, Jamshid Pourazar, Anders Blomberg, Anne Lindberg, Mikael Ringh, Michael Hagemann-Jensen, Tomas J. Ekstrom, Annelie F. Behndig, Erik Melen
Summary: DNA methylation patterns in chronic obstructive pulmonary disease (COPD) were investigated using an epigenome-wide association study on bronchoalveolar lavage (BAL) cells. The study identified differential methylation sites associated with COPD, and functional analysis revealed biologically plausible pathways and gene relationships. Integration with mRNA data showed a strong functional readout for relevant genes. The study also found colocalization between differential methylation sites and COPD-associated SNPs, suggesting joint genetic and epigenetic pathways related to the disease.
AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY
(2022)
Review
Pharmacology & Pharmacy
Marija Gredic, Isabel Blanco, Gabor Kovacs, Zsuzsanna Helyes, Peter Ferdinandy, Horst Olschewski, Joan Albert Barbera, Norbert Weissmann
Summary: This article summarizes the pathophysiology and treatment options for PH in COPD patients, pointing out that current research still does not fully understand its underlying mechanisms, and some of the treatment methods tested in clinical settings have not been effective. Preclinical studies have proposed some treatment approaches.
BRITISH JOURNAL OF PHARMACOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Lucas A. Gillenwater, Katerina J. Kechris, Katherine A. Pratte, Nichole Reisdorph, Irina Petrache, Wassim W. Labaki, Wanda O'Neal, Jerry A. Krishnan, Victor E. Ortega, Dawn L. DeMeo, Russell P. Bowler
Summary: Sex-specific differences in lung disease, response to treatment, and metabolic mechanisms driving these differences are still poorly understood, with women with COPD having distinct patterns compared to men. While some targeted metabolite studies have identified sex-specific compounds in COPD, the overall effect of COPD on systemic metabolism based on gender has not been fully explored.
Article
Critical Care Medicine
Jeffrey T-J Huang, Erin Cant, Holly R. Keir, Alun K. Barton, Elena Kuzmanova, Morven Shuttleworth, Jennifer Pollock, Simon Finch, Eva Polverino, Mathieu Bottier, Alison J. Dicker, Amelia Shoemark, James D. Chalmers
Summary: This study investigated the sputum microbiome and proteome in patients with bronchiectasis, COPD, and the COPD-bronchiectasis association, proposing five endotypes with differential inflammatory, mucin, and microbiological features. The key traits related to the COPD-bronchiectasis association include neutrophilic inflammation, differential mucin expression, and Gram-negative infection.
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2022)
Article
Biochemical Research Methods
Loan Vulliard, Joel Hancock, Anton Kamnev, Christopher W. Fell, Joana Ferreira da Silva, Joanna Loizou, Vanja Nagy, Loic Dupre, Joerg Menche
Summary: BioProfiling.jl is an efficient end-to-end solution for compiling and filtering informative morphological profiles in Julia. It provides necessary data structures and helper functions for analyzing and visualizing profiles, as well as robust statistical methods for quantifying the significance of observed changes. By analyzing a chemical imaging screen, this package demonstrates the informative nature of morphological profiles in understanding compound mechanisms of action.
Editorial Material
Genetics & Heredity
Harald H. H. W. Schmidt, Joerg Menche
Review
Genetics & Heredity
Salvo Danilo Lombardo, Ivan Fernando Wangsaputra, Jorg Menche, Adam Stevens
Summary: This article highlights the importance of the early developmental phase for human health and disease, focusing on the integration and analysis methods for studying transcriptomic and epigenetic processes relevant to the periconceptional period.
Article
Multidisciplinary Sciences
Tunde Pacza, Mayara L. Martins, Maha Rockaya, Katalin Muller, Ayan Chatterjee, Albert-Laszlo Barabasi, Jozsef Baranyi
Summary: This study develops a database called MilkyBase that contains the biochemical composition of human milk. The data are selected, digitized, and curated using both machine-learning and manual methods. The database allows users to find patterns in milk composition based on various factors and provides a platform for users to input their own data. The database is user-friendly and facilitates statistical analysis, uncertainty quantification, and prediction of dynamic compositions.
Article
Multidisciplinary Sciences
Hao Wu, Xiangyi Meng, Michael M. Danziger, Sean P. Cornelius, Hui Tian, Albert-Laszlo Barabasi
Summary: The understanding of recovery processes in power distribution grids is limited by the lack of realistic outage data, especially large-scale blackout datasets. By analyzing data from three electrical companies across the United States, researchers found that the recovery duration of an outage is connected with the downtime of its nearby outages and blackout intensity, but is independent of the number of customers affected. They presented a cluster-based recovery framework to analyze the dependence between outages and interpret the dominant role blackout intensity plays in recovery.
NATURE COMMUNICATIONS
(2022)
Article
Medicine, Research & Experimental
Bradley M. Wertheim, Rui-Sheng Wang, Christelle Guillermier, Christiane V. R. Huetter, William M. Oldham, Joerg Menche, Matthew L. Steinhauser, Bradley A. Maron
Summary: In pulmonary arterial hypertension (PAH), there is an inflammation-promoted fibroproliferative pulmonary vasculopathy. This study analyzed the transcriptome of pulmonary artery endothelial cells (PAECs) in PAH and integrated the data with human gene ontology pathways. The analysis showed that glucose and proline pathways are functionally relevant in PAH pathobiology, and this observation was validated using imaging mass spectrometry to map and quantify glucose and proline utilization in the PAH pulmonary vasculature. This study reveals that anabolic utilization of glucose and proline is fundamental in the vascular pathology of PAH.
Article
Multidisciplinary Sciences
Csaba Both, Nima Dehmamy, Rose Yu, Albert-Laszlo Barabasi
Summary: Graph layout algorithms are crucial in visualizing complex networks, but the current force-directed layout (FDL) algorithm has limitations in terms of computational complexity and layout interpretability. This study proposes using Graph Neural Networks (GNN) to accelerate FDL, resulting in significant speed improvement and more informative layouts. The use of deep learning in network visualization can also have implications for other optimization problems.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Giulia Menichetti, Babak Ravandi, Dariush Mozaffarian, Albert-Laszlo Barabasi
Summary: This study introduces a machine learning algorithm that accurately predicts the degree of processing for any food, indicating that over 73% of the US food supply is ultra-processed. The research shows that increased reliance on ultra-processed food is associated with various health issues and replacing these foods with less processed alternatives can significantly reduce their negative health implications. Thus, providing information on the degree of processing could improve population health.
NATURE COMMUNICATIONS
(2023)
Article
Environmental Sciences
Federica Lamberto, Bachuki Shashikadze, Radwa Elkhateib, Salvo Danilo Lombardo, Alex Horanszky, Andrea Balogh, Kornel Kistamas, Melinda Zana, Joerg Menche, Thomas Froehlich, Andras Dinnyes
Summary: This study investigated the effects of environmentally relevant doses of Bisphenol A (BPA) on developing cardiomyocytes using a human induced pluripotent stem cell (hiPSC)-derived model. The results showed that long-term treatment with low doses of BPA interferes with hiPSC-CMs functionality and alters the surrounding cellular environment, leading to potential diseases. This study contributes to the understanding of BPA effects on developing human foetal cardiomyocytes and provides a suitable model for environmental chemical hazard and risk assessment.
ENVIRONMENTAL POLLUTION
(2023)
Article
Multidisciplinary Sciences
Deisy Morselli Gysi, Albert-Laszlo Barabasi
Summary: Combining interactions mediated by noncoding RNAs (ncRNAs) with protein-protein interactions (PPI) improves the identification of disease modules and reveals previously undetectable disease relationships and comorbidity patterns.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Julia Guthrie, Sevgi Koestel Bal, Salvo Danilo Lombardo, Felix Mueller, Celine Sin, Christiane V. R. Huetter, Joerg Menche, Kaan Boztug
Summary: This study utilizes a network-based approach to integrate 186 genetic immune diseases into a comprehensive map of human immune dysregulation called AutoCore. AutoCore is divided into 19 endotypes corresponding to cohesive disease subgroups, providing a molecular mechanism-based disease classification and therapeutic targeting.
Article
Computer Science, Interdisciplinary Applications
Christiane V. R. Huetter, Celine Sin, Felix Mueller, Joerg Menche
Summary: Networks offer a visual representation for complex systems, where important characteristics can be recognized visually. However, traditional network layout algorithms have difficulty in interpreting and controlling the precise position of nodes within a layout. In this study, we propose an approach to directly encode network characteristics into node positions, which can be used to elucidate structure-to-function relationships in large-scale biological networks.
NATURE COMPUTATIONAL SCIENCE
(2022)
Article
Food Science & Technology
Giulia Menichetti, Albert-Laszlo Barabasi
Summary: This study quantifies the nutrient concentrations in food using a mathematical model and proposes a method to fill in missing values in food composition databases. The research shows that the concentration of each nutrient in food follows a universal scaling law, which can be explained by biochemical constraints. The findings provide a mathematical basis for understanding the impact of food processing on nutrient balance and health effects.
Article
Chemistry, Physical
Marianne Lahnsteiner, Michael Caldera, Hipassia M. Moura, D. Alonso Cerron-Infantes, Jerome Roeser, Thomas Konegger, Arne Thomas, Jorg Menche, Miriam M. Unterlass
Summary: The study focused on the hydrothermal polymerization of PI networks using H2O and comonomers TAPB and PMA, resulting in highly stable monoliths with unique hierarchical porosity. A hypothesis for morphology formation and evolution was devised through extensive micromorphological study, expert interpretation of SEM images, and computational image analysis. The upscaled HTP of PI(TAPB-PMA) allowed for the synthesis of dense cylindrical specimens without harmful solvents, showcasing the full route from synthesis to final material.
JOURNAL OF MATERIALS CHEMISTRY A
(2021)
Article
Respiratory System
Katherine A. Pratte, Jeffrey L. Curtis, Katerina Kechris, David Couper, Michael H. Cho, Edwin K. Silverman, Dawn L. DeMeo, Frank C. Sciurba, Yingze Zhang, Victor E. Ortega, Wanda K. O'Neal, Lucas A. Gillenwater, David A. Lynch, Eric A. Hoffman, John D. Newell, Alejandro P. Comellas, Peter J. Castaldi, Bruce E. Miller, Simon D. Pouwels, Nick H. T. ten Hacken, Rainer Bischoff, Frank Klont, Prescott G. Woodruff, Robert Paine, R. Graham Barr, John Hoidal, Claire M. Doerschuk, Jean-Paul Charbonnier, Ruby Sung, Nicholas Locantore, John G. Yonchuk, Sean Jacobson, Ruth Tal-singer, Debbie Merrill, Russell P. Bowler
Summary: sRAGE is associated with emphysema and airflow obstruction, with lower sRAGE levels linked to a COPD diagnosis, reduced FEV1, and increased emphysema severity. Genetic variability may influence sRAGE measurements in non-white populations.
RESPIRATORY RESEARCH
(2021)