Article
Biology
Hemant Kumar Joon, Anamika Thalor, Dinesh Gupta
Summary: This study demonstrates the potential importance of an integrated approach involving machine learning and system biology in identifying novel biomarkers for lung squamous cell carcinoma (LUSC).
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Biology
Stephen Meek, Tom Watson, Lel Eory, Gus McFarlane, Felicity J. Wynne, Stephen McCleary, Laura E. M. Dunn, Emily M. Charlton, Chloe Craig, Barbara Shih, Tim Regan, Ryan Taylor, Linda Sutherland, Anton Gossner, Cosmin Chintoan-Uta, Sarah Fletcher, Philippa M. Beard, Musa A. Hassan, Finn Grey, Jayne C. Hope, Mark P. Stevens, Monika Nowak-Imialek, Heiner Niemann, Pablo J. Ross, Christine Tait-Burkard, Sarah M. Brown, Lucas Lefevre, Gerard Thomson, Barry W. McColl, Alistair B. Lawrence, Alan L. Archibald, Falko Steinbach, Helen R. Crooke, Xuefei Gao, Pentao Liu, Tom Burdon
Summary: This study investigates the potential of porcine pluripotent stem cells to provide a limitless source of macrophages, demonstrating their molecular and functional characteristics, as well as their susceptibility to infection by pig pathogens. The study also shows the successful application of CRISPR/Cas9 gene editing in these cells, presenting new opportunities for researching host-pathogen interactions in pigs.
Article
Hematology
Hui Shi, Han He, Lei Cui, Egle Kvedaraite, Zhilei Bian, Tao Huang, Christopher Z. W. Lee, Zhigang Li, Jian He, Yandong Gong, Zongcheng Li, Jie Zhou, Yang Zeng, Xianlong Li, Yanli Ni, Zhijie Bai, Chen Liu, Na Li, Honghao Ma, Dong Wang, Yu Lan, Florent Ginhoux, Rui Zhang, Bing Liu
Summary: The study on Langerhans cell histiocytosis (LCH) analyzed samples from 217 pediatric patients and found a correlation between decreased frequency of specific immune cell populations and disease severity. Single-cell RNA sequencing identified changes in gene expression in the presence of BRAF(V600E). Treatment with BRAF inhibitor dabrafenib showed inhibition of MAPK cascade, inflammation prevention, and regulation of cellular metabolism.
Article
Medicine, Research & Experimental
Jingqi Liu, Pan Li, Jiaqi Zhu, Feiyan Lin, Jiahang Zhou, Bing Feng, Xinyu Sheng, Xiaowei Shi, Qiaoling Pan, Jiong Yu, Jianqing Gao, Lanjuan Li, Hongcui Cao
Summary: This study identified eight subsets of mononuclear phagocytes recruited to LPS-challenged lungs and found that MSCs can reduce the number of M1 macrophages and CD38(+) mo-DCs, leading to decreased mortality in ALI mice.
Article
Oncology
Francesca Minnai, Sara Noci, Marco Chierici, Chiara Elisabetta Cotroneo, Barbara Bartolini, Matteo Incarbone, Davide Tosi, Giovanni Mattioni, Giuseppe Jurman, Tommaso A. Dragani, Francesca Colombo
Summary: Emerging evidence suggests that the prognosis of patients with lung adenocarcinoma can be determined from germline variants and transcript levels in nontumoral lung tissue. Gene expression data from noninvolved lung tissue of 483 lung adenocarcinoma patients were analyzed, and a signature of transcripts associated with lung adenocarcinoma outcome was identified. Pathway analysis indicated enrichment of ECM components. Genetic predisposition to lung adenocarcinoma outcome was found to be present in patients' noninvolved lung tissue.
Article
Cell Biology
Anastasiia Gainullina, Denis A. Mogilenko, Li-Hao Huang, Helena Todorov, Vipin Narang, Ki-Wook Kim, Lim Sheau Yng, Andrew Kent, Baosen Jia, Kumba Seddu, Karen Krchma, Jun Wu, Karine Crozat, Elena Tomasello, Regine Dress, Peter See, Charlotte Scott, Sophie Gibbings, Geetika Bajpai, Jigar V. Desai, Barbara Maier, Sebastien This, Peter Wang, Stephanie Vargas Aguilar, Lucie Poupel, Sebastien Dussaud, Tyng-An Zhou, Veronique Angeli, J. Magarian Blander, Kyunghee Choi, Marc Dalod, Ivan Dzhagalov, Emmanuel L. Gautier, Claudia Jakubzick, Kory Lavine, Michail S. Lionakis, Helena Paidassi, Michael H. Sieweke, Florent Ginhoux, Martin Guilliams, Christophe Benoist, Miriam Merad, Gwendalyn J. Randolph, Alexey Sergushichev, Maxim N. Artyomov
Summary: This study focuses on the diversity and metabolic variability of mononuclear phagocyte (MNP) subpopulations. Through metabolic network analysis of large-scale transcriptional datasets, it was found that cholesterol synthesis is particularly active in migratory dendritic cells, while glutathione synthesis is essential for cysteinyl leukotriene production by peritoneal and lung macrophages.
Article
Computer Science, Information Systems
Bulent Haznedar, Nihat Y. Simsek
Summary: In this study, a deep learning model based on deep neural network architecture was proposed and utilized to analyze lung and renal cell cancer RNA-Seq datasets. The results showed that the proposed model achieved excellent performance in analyzing these datasets, outperforming other commonly-used machine learning algorithms in terms of accuracy.
Article
Mathematics
Gerardo Alfonso Perez, Raquel Castillo
Summary: This paper presents an algorithm that uses machine learning techniques to accurately identify patients with ILD-SSc and identifies 172 genes related to the disease. The algorithm is also able to differentiate between different variants of the disease, which has significance for treatment.
Article
Cardiac & Cardiovascular Systems
Keiji Yamanashi, Akihiro Ohsumi, Hiromi Oda, Satona Tanaka, Yoshito Yamada, Daisuke Nakajima, Hiroshi Date
Summary: The objective of this study was to investigate the depletion of mononuclear phagocytes and the attenuation of ischemia-reperfusion injury by clodronate-liposome during ex vivo lung perfusion. The experiments determined the number of mononuclear phagocytes in flushed grafts using flow cytometry and administered clodronate-liposome into the perfusate during ex vivo lung perfusion. The results showed a significant reduction in the number of mononuclear phagocytes in the clodronate group, improved lung function, and reduced lung injury.
JOURNAL OF THORACIC AND CARDIOVASCULAR SURGERY
(2023)
Article
Biochemical Research Methods
Javier Bajo-Morales, Juan Manuel Galvez, Juan Carlos Prieto-Prieto, Luis Javier Herrera, Ignacio Rojas, Daniel Castillo-Secilla
Summary: This study describes and implements a machine learning methodology to evaluate the compatibility between RNA-Seq and Microarray sequencing technologies, and its application in identifying and classifying lung cancer subtypes. The results show that predictive models built using different technologies can accurately classify samples, and strong gene signatures related to lung cancer have been discovered.
CURRENT BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Nuojin Cheng, Ashley J. Schulte, Fadil Santosa, Jong Hyuk Kim
Summary: Angiosarcomas are rare soft-tissue sarcomas with poor clinical outcomes due to their aggressive behavior and high metastatic potential. Hemangiosarcomas in dogs share features with human angiosarcomas, characterized by irregular vascular channels and a mixture of endothelial cells. Machine learning models using transcriptomic data show promise for diagnosing hemangiosarcoma and identifying novel gene signatures for potential applications in treating this vascular malignancy.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Health Care Sciences & Services
Jiande Wu, Chindo Hicks
Summary: The study proposed a new approach to classify triple negative breast cancer and non-triple negative breast cancer patients using machine learning methods, with the Support Vector Machine algorithm demonstrating higher accuracy and fewer misclassification errors in classifying breast cancer types.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Review
Biochemical Research Methods
Sreya Vadapalli, Habiba Abdelhalim, Saman Zeeshan, Zeeshan Ahmed
Summary: Precision medicine utilizes genetic, environmental, and lifestyle factors to accurately diagnose and treat diseases in specific patient groups. The integration of genetics into precision medicine is a complex and data-rich aspect. The use of artificial intelligence (AI) and machine learning (ML) methods is crucial for successfully incorporating genetics into precision medicine across diverse populations and diseases. This review compares and analyzes the scientific objectives, methodologies, datasets, data sources, ethics, and gaps of AI/ML approaches in genomics and precision medicine, identifying 32 different AI/ML approaches applied in various genomics studies.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Pharmacology & Pharmacy
Rui Xuan Huang, Damrongrat Siriwanna, William C. Cho, Tsz Kin Wan, Yan Rong Du, Adam N. Bennett, Qian Echo He, Jun Dong Liu, Xiao Tai Huang, Kei Hang Katie Chan
Summary: In this study, a pipeline based on machine learning was developed to predict potential target genes for LUAD and discover potential drugs for its treatment through drug repositioning. The pipeline achieved good predictive performance and identified several potential therapeutic drugs for LUAD.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Oncology
Adrian Mosquera Orgueira, Miguel Cid Lopez, Andres Peleteiro Raindo, Aitor Abuin Blanco, Jose Angel Diaz Arias, Marta Sonia Gonzalez Perez, Beatriz Antelo Rodriguez, Laura Bao Perez, Roi Ferreiro Ferro, Carlos Aliste Santos, Manuel Mateo Perez Encinas, Maximo Francisco Fraga Rodriguez, Claudio Cerchione, Pablo Mozas, Jose Luis Bello Lopez
Summary: This study utilized machine learning tools to analyze gene expression data and successfully created a model that can provide individualized predictions of overall survival in follicular lymphoma patients. The integration of this model with m7-FLIPI and age achieved high prediction accuracies and a simplified approach identified distinct groups with significantly different survival outcomes.
FRONTIERS IN ONCOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Irene Sanchez-Martin, Pedro Magalhaes, Parisa Ranjzad, Ahmed Fatmi, Fabrice Richard, Thien Phong Vu Manh, Andrew J. Saurin, Guylene Feuillet, Colette Denis, Adrian S. Woolf, Joost P. Schanstra, Petra Zurbig, Xavier Caubit, Laurent Fasano
Summary: This study provides the first evidence that Tshz3 haploinsufficiency leads to cellular, molecular and functional abnormalities in the adult mouse kidney.
HUMAN MOLECULAR GENETICS
(2022)
Article
Multidisciplinary Sciences
Alba Frias-De-Diego, Elisa Crisci
Summary: This study compared visual CPE observation via microscopy, ICC staining, and crystal violet staining for determining the titers of CPE-forming viruses. Both crystal violet and ICC staining were found to be more accurate than visual CPE detection.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2022)
Article
Cell Biology
Maeva Dupont, Stella Rousset, Thien-Phong Vu Manh, Sarah Catherine Monard, Karine Pingris, Shanti Souriant, Zoi Vahlas, Tomas Velez, Renaud Poincloux, Isabelle I. Maridonneau-Parini, Olivier Neyrolles, Geanncarlo Lugo-Villarino, Christel Verollet
Summary: While tuberculosis is a risk factor for HIV-1-infected individuals, the mechanisms by which Mycobacterium tuberculosis worsens HIV-1 pathogenesis still need to be fully understood. Recent research has shown that HIV-1 infection and spread are exacerbated in macrophages exposed to TB-associated microenvironments.
JOURNAL OF LEUKOCYTE BIOLOGY
(2022)
Review
Agriculture, Dairy & Animal Science
Brittany M. Pecoraro, Diego F. Leal, Alba Frias-De-Diego, Matthew Browning, Jack Odle, Elisa Crisci
Summary: Selenium is an essential trace mineral with strong antioxidant, anti-inflammatory, and potential antimicrobial capacities. It is primarily present in selenoproteins as selenocysteine, playing a crucial role in maintaining homeostasis. Dietary selenium supplementation, in both organic and inorganic forms, improves growth performance, immune function, and meat quality in food animals like pigs. Additionally, selenium exhibits antiviral activity by protecting immune cells and inhibiting viral replication. However, further in vivo and in vitro studies are needed to explore the full potential of selenium as an antiviral agent.
JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
Georgia Ntasi, Sara Sbriglia, Rossana Pitocchi, Roberto Vinciguerra, Chiara Melchiorre, Laura Dello Ioio, Giancarlo Fatigati, Emanuele Crisci, Ilaria Bonaduce, Andrea Carpentieri, Gennaro Marino, Leila Birolo
Summary: Animal glues are commonly used in restoration, and their performance is determined by the adhesive properties of collagen. Mass spectrometry techniques were used to characterize the protein components of homemade and commercial glues. The study identified the animal origin of the glues and distinguished between hide and bone glue based on the presence of collagen type III. The analysis of chemical modifications showed variations among different glues. These findings have analytical significance in the characterization of collagen-based materials and can assist restorers in selecting appropriate materials for conservation treatments.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Virology
Elisa Crisci
Summary: This paper focuses on the career of Dr. Ilaria Capua, an exceptional woman virologist. It highlights her major achievements, awards, and significant events that have shaped her scientific and political career. The paper discusses her contributions to the study of viral zoonoses, particularly the influenza virus, as well as her commitment to open access and data sharing. It introduces her concept of Circular Health and emphasizes her role as a role model for young women scientists and their empowerment.
Article
Cell Biology
Payel Banerjee, Paul Joly, Luc Jouneau, Yan Jaszczyszyn, Mickael Bourge, Pierre Affaticati, Jean-Pierre Levraud, Pierre Boudinot, Jean-Stephane Joly
Summary: In this study, the recruitment of cells following optic tectum (OT) injury in zebrafish was investigated. The results showed that deep-laser injury did not induce massive recruitment of cells, while surface-laser injury led to the migration of different cell types to the injury site. This study provides important insights into the mechanisms of meninges repair in zebrafish and potentially in mammalian meninges.
Article
Gastroenterology & Hepatology
Virginie Millet, Thomas Gensollen, Michael Maltese, Melanie Serrero, Nathalie Lesavre, Christophe Bourges, Christophe Pitaval, Sophie Cadra, Lionel Chasson, Thien Phong Vu Man, Marion Masse, Juan Jose Martinez-Garcia, Fabrice Tranchida, Laetitia Shintu, Konrad Mostert, Erick Strauss, Patricia Lepage, Mathias Chamaillard, Achille Broggi, Laurent Peyrin-Biroulet, Jean-Charles Grimaud, Philippe Naquet, Franck Galland
Summary: This study shows that the overexpression of Vnn1 is associated with the severity of IBD. VIVA mice are resistant to experimental colitis, and the pantetheinase activity of Vnn1 has a protective effect on colonocytes, enhancing CoA regeneration and metabolic adaptation. It also promotes the production of microbiota-dependent short chain fatty acids, especially butyrate, which regulates mucosal energetics and is reduced in patients with IBD. The induction of Vnn1/VNN1 during colitis is a compensatory mechanism to strengthen the mucosal barrier, and enhancing vitamin B-5-driven metabolism may improve mucosal healing and increase the efficacy of anti-inflammatory therapy.
Article
Microbiology
Jessica Proctor, Iman Wolf, David Brodsky, Lizette M. Cortes, Alba Frias-De-Diego, Glen W. Almond, Elisa Crisci, Tatiane Terumi Negrao Watanabe, James M. Hammer, Tobias Kaeser
Summary: This study investigated the efficacy and immunogenicity of a modified live virus vaccine against four heterologous PRRSV-2 strains. The vaccine showed varying degrees of efficacy and immunogenicity, providing cross-protection and inducing a strong immune response and antibody production.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Julie Hodin, Christof Lind, Anne Marmagne, Christelle Espagne, Michele Wolfe Bianchi, Alexis De Angeli, Fadi Abou-Choucha, Mickael Bourge, Fabien Chardon, Sebastien Thomine, Sophie Filleur
Summary: The CLCa exchanger on the vacuole plays a critical role in plant metabolism and development. Mutant CLCaE203A not only affects water homeostasis and nitrate accumulation in plants but also enhances nitrogen uptake and use efficiency.
Article
Virology
Alba Frias-De-Diego, Jessica M. M. Gilbertie, Frank Scholle, Sarah Dejarnette, Elisa Crisci
Summary: This study evaluates the antiviral effect of a novel platelet-rich plasma-derived biologic called BIO-PLYTM against PRRS virus. The results show that BIO-PLYTM significantly reduces viral load and infectious viral particles, and exhibits immunomodulatory capacity.
Article
Immunology
Michael Valente, Nils Collinet, Thien-Phong Vu Manh, Dimitri Popoff, Khalissa Rahmani, Karima Naciri, Gilles Bessou, Rejane Rua, Laurine Gil, Cyrille Mionnet, Pierre Milpied, Elena Tomasello, Marc Dalod
Review
Immunology
Andrew R. Kick, Alicyn F. Grete, Elisa Crisci, Glen W. Almond, Tobias Kaeser
Summary: PRRSV is a persistent issue in the global pig industry. Although vaccinations show some benefits, the specific immune correlates of protection (CoP) have not been clearly defined. We propose four hypotheses for CoP in PRRSV research, which can guide future vaccine design and evaluation.
Article
Plant Sciences
Beatrix Horvath, Berivan Gungor, Monika Toth, Agota Domonkos, Ferhan Ayaydin, Farheen Saifi, Yuhui Chen, Janos Barnabas Biro, Mickael Bourge, Zoltan Szabo, Zoltan Toth, Rujin Chen, Peter Kalo
Summary: By characterizing and analyzing three ineffective nitrogen-fixing Medicago truncatula mutants, we discovered that Mtsym19 and Mtsym20 mutants have defects in the same peptide NCR-new35, and the lack of NCR343 is responsible for the ineffective symbiosis of NF-FN9363. We found that the expression of NCR-new35 is significantly lower and limited to the transition zone of the nodule compared with other crucial NCRs. The fluorescent protein-tagged versions of NCR343 and NCR-new35 localized to the symbiotic compartment.
Article
Biochemical Research Methods
Rupert Dodkins, John R. Delaney, Tess Overton, Frank Scholle, Alba Frias-De-Diego, Elisa Crisci, Nafisa Huq, Ingo Jordan, Jason T. Kimata, Teresa Findley, Ilya G. Goldberg
Summary: Infectivity assays are crucial for the development of viral vaccines, antiviral therapies, and biological manufacturing. An automated viral infectivity assay (AVIA) utilizing convolutional neural networks and high-throughput brightfield microscopy on 96-well plates has been developed to quantify infection phenotypes rapidly and accurately without sample preparation. The AVIA demonstrates sensitivity and precision comparable to or better than conventional assays and has the potential to be a rapid and broad-spectrum tool for virus characterization and identification.